PDB Short entry for 3LDO HEADER CHAPERONE 13-JAN-10 3LDO TITLE CRYSTAL STRUCTURE OF HUMAN GRP78 (70KDA HEAT SHOCK PROTEIN 5 / BIP) TITLE 2 ATPASE DOMAIN IN COMPLEX WITH AMPPNP COMPND MOL_ID: 1; COMPND 2 MOLECULE: 78 KDA GLUCOSE-REGULATED PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: ATPASE DOMAIN (RESIDUES 26-407); COMPND 5 SYNONYM: GRP 78, HEAT SHOCK 70 KDA PROTEIN 5, IMMUNOGLOBULIN HEAVY COMPND 6 CHAIN-BINDING PROTEIN, BIP, ENDOPLASMIC RETICULUM LUMENAL CA(2+)- COMPND 7 BINDING PROTEIN GRP78; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HSPA5, GRP78; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-4T-1 KEYWDS GRP78, HSP70, HSC70, CHAPERONE, HEAT SHOCK, PROTEIN FOLDING, ATP- KEYWDS 2 BINDING, ADENOSINE, NUCLEOSIDE, NUCLEOTIDE-BINDING, STRESS RESPONSE, KEYWDS 3 SMALL MOLECULE INHIBITOR, SELECTIVITY, ENDOPLASMIC RETICULUM, KEYWDS 4 PHOSPHOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.DOKURNO,A.E.SURGENOR,T.SHAW,A.T.MACIAS,A.J.MASSEY,D.S.WILLIAMSON REVDAT 3 29-JUN-11 3LDO 1 JRNL REVDAT 2 08-JUN-11 3LDO 1 JRNL REVDAT 1 26-JAN-11 3LDO 0 JRNL AUTH A.T.MACIAS,D.S.WILLIAMSON,N.ALLEN,J.BORGOGNONI,A.CLAY, JRNL AUTH 2 Z.DANIELS,P.DOKURNO,M.J.DRYSDALE,G.L.FRANCIS,C.J.GRAHAM, JRNL AUTH 3 R.HOWES,N.MATASSOVA,J.B.MURRAY,R.PARSONS,T.SHAW, JRNL AUTH 4 A.E.SURGENOR,L.TERRY,Y.WANG,M.WOOD,A.J.MASSEY JRNL TITL ADENOSINE-DERIVED INHIBITORS OF 78 KDA GLUCOSE REGULATED JRNL TITL 2 PROTEIN (GRP78) ATPASE: INSIGHTS INTO ISOFORM SELECTIVITY. JRNL REF J.MED.CHEM. V. 54 4034 2011 JRNL REFN ISSN 0022-2623 JRNL PMID 21526763 JRNL DOI 10.1021/JM101625X REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 48474 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.300 REMARK 3 FREE R VALUE TEST SET COUNT : 3799 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3376 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.42 REMARK 3 BIN R VALUE (WORKING SET) : 0.2280 REMARK 3 BIN FREE R VALUE SET COUNT : 257 REMARK 3 BIN FREE R VALUE : 0.3030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5883 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 62 REMARK 3 SOLVENT ATOMS : 499 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.03000 REMARK 3 B22 (A**2) : -0.97000 REMARK 3 B33 (A**2) : -0.40000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.16000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.215 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.187 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.133 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.548 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.934 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.895 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6039 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8168 ; 1.493 ; 1.952 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 761 ; 5.808 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 273 ;36.945 ;25.018 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1070 ;16.448 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;14.877 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 933 ; 0.103 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4506 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2866 ; 0.212 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4139 ; 0.301 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 500 ; 0.168 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 69 ; 0.183 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 22 ; 0.173 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3884 ; 0.917 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6083 ; 1.470 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2406 ; 2.363 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2085 ; 3.549 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3LDO COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JAN-10. REMARK 100 THE RCSB ID CODE IS RCSB057148. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAR-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9730 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55779 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.31600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS BUFFER, 25% PEG3350, 0.1M REMARK 280 NA,K TARTRATE, PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 37.28150 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 24 REMARK 465 SER A 25 REMARK 465 GLY B 24 REMARK 465 SER B 25 REMARK 465 GLY B 407 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP A 26 CG OD1 OD2 REMARK 470 LEU A 84 CG CD1 CD2 REMARK 470 LYS A 272 CG CD CE NZ REMARK 470 LYS A 273 CG CD CE NZ REMARK 470 GLU A 308 CG CD OE1 OE2 REMARK 470 ARG A 386 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 272 CG CD CE NZ REMARK 470 ASN B 282 CG OD1 REMARK 470 ARG B 306 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 352 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ASN B 87 O HOH B 524 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 105 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 87 69.52 -117.84 REMARK 500 THR A 124 -6.39 74.73 REMARK 500 ASN A 239 65.94 37.00 REMARK 500 THR A 274 -135.93 -110.20 REMARK 500 VAL A 278 -39.68 -31.90 REMARK 500 ASN B 47 60.00 37.96 REMARK 500 LEU B 84 58.28 -115.64 REMARK 500 THR B 124 -7.44 78.28 REMARK 500 LYS B 280 4.39 -62.77 REMARK 500 SER B 301 -81.64 -77.87 REMARK 500 GLN B 302 172.71 -59.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER B 86 ASN B 87 134.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 SER B 86 24.3 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ANP A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ANP B 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3LDL RELATED DB: PDB REMARK 900 RELATED ID: 3LDN RELATED DB: PDB REMARK 900 RELATED ID: 3LDP RELATED DB: PDB REMARK 900 RELATED ID: 3LDQ RELATED DB: PDB DBREF 3LDO A 26 407 UNP P11021 GRP78_HUMAN 26 407 DBREF 3LDO B 26 407 UNP P11021 GRP78_HUMAN 26 407 SEQADV 3LDO GLY A 24 UNP P11021 EXPRESSION TAG SEQADV 3LDO SER A 25 UNP P11021 EXPRESSION TAG SEQADV 3LDO GLY B 24 UNP P11021 EXPRESSION TAG SEQADV 3LDO SER B 25 UNP P11021 EXPRESSION TAG SEQRES 1 A 384 GLY SER ASP VAL GLY THR VAL VAL GLY ILE ASP LEU GLY SEQRES 2 A 384 THR THR TYR SER CYS VAL GLY VAL PHE LYS ASN GLY ARG SEQRES 3 A 384 VAL GLU ILE ILE ALA ASN ASP GLN GLY ASN ARG ILE THR SEQRES 4 A 384 PRO SER TYR VAL ALA PHE THR PRO GLU GLY GLU ARG LEU SEQRES 5 A 384 ILE GLY ASP ALA ALA LYS ASN GLN LEU THR SER ASN PRO SEQRES 6 A 384 GLU ASN THR VAL PHE ASP ALA LYS ARG LEU ILE GLY ARG SEQRES 7 A 384 THR TRP ASN ASP PRO SER VAL GLN GLN ASP ILE LYS PHE SEQRES 8 A 384 LEU PRO PHE LYS VAL VAL GLU LYS LYS THR LYS PRO TYR SEQRES 9 A 384 ILE GLN VAL ASP ILE GLY GLY GLY GLN THR LYS THR PHE SEQRES 10 A 384 ALA PRO GLU GLU ILE SER ALA MET VAL LEU THR LYS MET SEQRES 11 A 384 LYS GLU THR ALA GLU ALA TYR LEU GLY LYS LYS VAL THR SEQRES 12 A 384 HIS ALA VAL VAL THR VAL PRO ALA TYR PHE ASN ASP ALA SEQRES 13 A 384 GLN ARG GLN ALA THR LYS ASP ALA GLY THR ILE ALA GLY SEQRES 14 A 384 LEU ASN VAL MET ARG ILE ILE ASN GLU PRO THR ALA ALA SEQRES 15 A 384 ALA ILE ALA TYR GLY LEU ASP LYS ARG GLU GLY GLU LYS SEQRES 16 A 384 ASN ILE LEU VAL PHE ASP LEU GLY GLY GLY THR PHE ASP SEQRES 17 A 384 VAL SER LEU LEU THR ILE ASP ASN GLY VAL PHE GLU VAL SEQRES 18 A 384 VAL ALA THR ASN GLY ASP THR HIS LEU GLY GLY GLU ASP SEQRES 19 A 384 PHE ASP GLN ARG VAL MET GLU HIS PHE ILE LYS LEU TYR SEQRES 20 A 384 LYS LYS LYS THR GLY LYS ASP VAL ARG LYS ASP ASN ARG SEQRES 21 A 384 ALA VAL GLN LYS LEU ARG ARG GLU VAL GLU LYS ALA LYS SEQRES 22 A 384 ARG ALA LEU SER SER GLN HIS GLN ALA ARG ILE GLU ILE SEQRES 23 A 384 GLU SER PHE TYR GLU GLY GLU ASP PHE SER GLU THR LEU SEQRES 24 A 384 THR ARG ALA LYS PHE GLU GLU LEU ASN MET ASP LEU PHE SEQRES 25 A 384 ARG SER THR MET LYS PRO VAL GLN LYS VAL LEU GLU ASP SEQRES 26 A 384 SER ASP LEU LYS LYS SER ASP ILE ASP GLU ILE VAL LEU SEQRES 27 A 384 VAL GLY GLY SER THR ARG ILE PRO LYS ILE GLN GLN LEU SEQRES 28 A 384 VAL LYS GLU PHE PHE ASN GLY LYS GLU PRO SER ARG GLY SEQRES 29 A 384 ILE ASN PRO ASP GLU ALA VAL ALA TYR GLY ALA ALA VAL SEQRES 30 A 384 GLN ALA GLY VAL LEU SER GLY SEQRES 1 B 384 GLY SER ASP VAL GLY THR VAL VAL GLY ILE ASP LEU GLY SEQRES 2 B 384 THR THR TYR SER CYS VAL GLY VAL PHE LYS ASN GLY ARG SEQRES 3 B 384 VAL GLU ILE ILE ALA ASN ASP GLN GLY ASN ARG ILE THR SEQRES 4 B 384 PRO SER TYR VAL ALA PHE THR PRO GLU GLY GLU ARG LEU SEQRES 5 B 384 ILE GLY ASP ALA ALA LYS ASN GLN LEU THR SER ASN PRO SEQRES 6 B 384 GLU ASN THR VAL PHE ASP ALA LYS ARG LEU ILE GLY ARG SEQRES 7 B 384 THR TRP ASN ASP PRO SER VAL GLN GLN ASP ILE LYS PHE SEQRES 8 B 384 LEU PRO PHE LYS VAL VAL GLU LYS LYS THR LYS PRO TYR SEQRES 9 B 384 ILE GLN VAL ASP ILE GLY GLY GLY GLN THR LYS THR PHE SEQRES 10 B 384 ALA PRO GLU GLU ILE SER ALA MET VAL LEU THR LYS MET SEQRES 11 B 384 LYS GLU THR ALA GLU ALA TYR LEU GLY LYS LYS VAL THR SEQRES 12 B 384 HIS ALA VAL VAL THR VAL PRO ALA TYR PHE ASN ASP ALA SEQRES 13 B 384 GLN ARG GLN ALA THR LYS ASP ALA GLY THR ILE ALA GLY SEQRES 14 B 384 LEU ASN VAL MET ARG ILE ILE ASN GLU PRO THR ALA ALA SEQRES 15 B 384 ALA ILE ALA TYR GLY LEU ASP LYS ARG GLU GLY GLU LYS SEQRES 16 B 384 ASN ILE LEU VAL PHE ASP LEU GLY GLY GLY THR PHE ASP SEQRES 17 B 384 VAL SER LEU LEU THR ILE ASP ASN GLY VAL PHE GLU VAL SEQRES 18 B 384 VAL ALA THR ASN GLY ASP THR HIS LEU GLY GLY GLU ASP SEQRES 19 B 384 PHE ASP GLN ARG VAL MET GLU HIS PHE ILE LYS LEU TYR SEQRES 20 B 384 LYS LYS LYS THR GLY LYS ASP VAL ARG LYS ASP ASN ARG SEQRES 21 B 384 ALA VAL GLN LYS LEU ARG ARG GLU VAL GLU LYS ALA LYS SEQRES 22 B 384 ARG ALA LEU SER SER GLN HIS GLN ALA ARG ILE GLU ILE SEQRES 23 B 384 GLU SER PHE TYR GLU GLY GLU ASP PHE SER GLU THR LEU SEQRES 24 B 384 THR ARG ALA LYS PHE GLU GLU LEU ASN MET ASP LEU PHE SEQRES 25 B 384 ARG SER THR MET LYS PRO VAL GLN LYS VAL LEU GLU ASP SEQRES 26 B 384 SER ASP LEU LYS LYS SER ASP ILE ASP GLU ILE VAL LEU SEQRES 27 B 384 VAL GLY GLY SER THR ARG ILE PRO LYS ILE GLN GLN LEU SEQRES 28 B 384 VAL LYS GLU PHE PHE ASN GLY LYS GLU PRO SER ARG GLY SEQRES 29 B 384 ILE ASN PRO ASP GLU ALA VAL ALA TYR GLY ALA ALA VAL SEQRES 30 B 384 GLN ALA GLY VAL LEU SER GLY HET ANP A 408 31 HET ANP B 501 31 HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER FORMUL 3 ANP 2(C10 H17 N6 O12 P3) FORMUL 5 HOH *499(H2 O) HELIX 1 1 GLY A 77 GLN A 83 1 7 HELIX 2 2 ASN A 87 GLU A 89 5 3 HELIX 3 3 ASP A 94 LEU A 98 5 5 HELIX 4 4 ASP A 105 LEU A 115 1 11 HELIX 5 5 ALA A 141 GLY A 162 1 22 HELIX 6 6 ASN A 177 ALA A 191 1 15 HELIX 7 7 GLU A 201 TYR A 209 1 9 HELIX 8 8 GLY A 210 ARG A 214 5 5 HELIX 9 9 GLY A 254 THR A 274 1 21 HELIX 10 10 ASP A 277 LYS A 280 5 4 HELIX 11 11 ASP A 281 LEU A 299 1 19 HELIX 12 12 ARG A 324 SER A 337 1 14 HELIX 13 13 THR A 338 SER A 349 1 12 HELIX 14 14 LYS A 352 ILE A 356 5 5 HELIX 15 15 GLY A 363 ARG A 367 5 5 HELIX 16 16 ILE A 368 PHE A 379 1 12 HELIX 17 17 GLU A 392 GLY A 407 1 16 HELIX 18 18 GLY B 77 GLN B 83 1 7 HELIX 19 19 ASP B 94 LEU B 98 5 5 HELIX 20 20 ASP B 105 LEU B 115 1 11 HELIX 21 21 ALA B 141 GLY B 162 1 22 HELIX 22 22 ASN B 177 ALA B 191 1 15 HELIX 23 23 GLU B 201 TYR B 209 1 9 HELIX 24 24 GLY B 210 ARG B 214 5 5 HELIX 25 25 GLY B 254 GLY B 275 1 22 HELIX 26 26 ASP B 277 LYS B 280 5 4 HELIX 27 27 ASP B 281 GLN B 302 1 22 HELIX 28 28 ARG B 324 SER B 337 1 14 HELIX 29 29 THR B 338 SER B 349 1 12 HELIX 30 30 LYS B 352 ILE B 356 5 5 HELIX 31 31 GLY B 363 ARG B 367 5 5 HELIX 32 32 ILE B 368 PHE B 379 1 12 HELIX 33 33 GLU B 392 SER B 406 1 15 SHEET 1 A 3 ARG A 49 ILE A 52 0 SHEET 2 A 3 TYR A 39 LYS A 46 -1 N VAL A 44 O GLU A 51 SHEET 3 A 3 THR A 62 PRO A 63 -1 O THR A 62 N SER A 40 SHEET 1 B 5 ARG A 49 ILE A 52 0 SHEET 2 B 5 TYR A 39 LYS A 46 -1 N VAL A 44 O GLU A 51 SHEET 3 B 5 VAL A 31 ASP A 34 -1 N ASP A 34 O CYS A 41 SHEET 4 B 5 HIS A 167 VAL A 172 1 O VAL A 169 N ILE A 33 SHEET 5 B 5 ASN A 194 ASN A 200 1 O ASN A 194 N ALA A 168 SHEET 1 C 3 ARG A 74 ILE A 76 0 SHEET 2 C 3 VAL A 66 PHE A 68 -1 N ALA A 67 O LEU A 75 SHEET 3 C 3 THR A 91 VAL A 92 -1 O VAL A 92 N VAL A 66 SHEET 1 D 3 LYS A 118 LYS A 122 0 SHEET 2 D 3 LYS A 125 ASP A 131 -1 O TYR A 127 N VAL A 120 SHEET 3 D 3 THR A 137 PHE A 140 -1 O PHE A 140 N ILE A 128 SHEET 1 E 4 VAL A 241 ASP A 250 0 SHEET 2 E 4 PHE A 230 ASP A 238 -1 N VAL A 232 O ASN A 248 SHEET 3 E 4 GLU A 217 LEU A 225 -1 N ILE A 220 O LEU A 235 SHEET 4 E 4 GLU A 358 VAL A 362 1 O VAL A 360 N LEU A 221 SHEET 1 F 2 GLN A 304 TYR A 313 0 SHEET 2 F 2 GLU A 316 THR A 323 -1 O GLU A 320 N ILE A 307 SHEET 1 G 3 ARG B 49 ILE B 52 0 SHEET 2 G 3 TYR B 39 LYS B 46 -1 N VAL B 44 O GLU B 51 SHEET 3 G 3 THR B 62 PRO B 63 -1 O THR B 62 N SER B 40 SHEET 1 H 5 ARG B 49 ILE B 52 0 SHEET 2 H 5 TYR B 39 LYS B 46 -1 N VAL B 44 O GLU B 51 SHEET 3 H 5 VAL B 31 ASP B 34 -1 N GLY B 32 O GLY B 43 SHEET 4 H 5 HIS B 167 VAL B 172 1 O VAL B 169 N ILE B 33 SHEET 5 H 5 ASN B 194 ASN B 200 1 O MET B 196 N ALA B 168 SHEET 1 I 3 ARG B 74 ILE B 76 0 SHEET 2 I 3 VAL B 66 PHE B 68 -1 N ALA B 67 O LEU B 75 SHEET 3 I 3 THR B 91 VAL B 92 -1 O VAL B 92 N VAL B 66 SHEET 1 J 3 LYS B 118 LYS B 122 0 SHEET 2 J 3 LYS B 125 ASP B 131 -1 O LYS B 125 N LYS B 122 SHEET 3 J 3 THR B 137 PHE B 140 -1 O PHE B 140 N ILE B 128 SHEET 1 K 4 VAL B 241 ASP B 250 0 SHEET 2 K 4 PHE B 230 ASP B 238 -1 N VAL B 232 O ASN B 248 SHEET 3 K 4 GLU B 217 LEU B 225 -1 N VAL B 222 O SER B 233 SHEET 4 K 4 GLU B 358 VAL B 362 1 O VAL B 362 N PHE B 223 SHEET 1 L 2 GLN B 304 TYR B 313 0 SHEET 2 L 2 GLU B 316 THR B 323 -1 O LEU B 322 N ALA B 305 SITE 1 AC1 31 ASP A 34 GLY A 36 THR A 37 THR A 38 SITE 2 AC1 31 TYR A 39 GLY A 226 GLY A 227 GLY A 228 SITE 3 AC1 31 THR A 229 GLY A 255 GLU A 293 LYS A 296 SITE 4 AC1 31 ARG A 297 SER A 300 GLY A 363 GLY A 364 SITE 5 AC1 31 SER A 365 ARG A 367 ILE A 368 ASP A 391 SITE 6 AC1 31 HOH A 418 HOH A 443 HOH A 483 HOH A 493 SITE 7 AC1 31 HOH A 519 HOH A 520 HOH A 605 HOH A 608 SITE 8 AC1 31 HOH A 642 HOH A 647 HOH A 650 SITE 1 AC2 29 ASP B 34 GLY B 36 THR B 37 THR B 38 SITE 2 AC2 29 TYR B 39 GLY B 226 GLY B 227 GLY B 228 SITE 3 AC2 29 THR B 229 GLY B 255 GLU B 293 LYS B 296 SITE 4 AC2 29 ARG B 297 SER B 300 GLY B 363 GLY B 364 SITE 5 AC2 29 SER B 365 ARG B 367 ILE B 368 ASP B 391 SITE 6 AC2 29 HOH B 409 HOH B 427 HOH B 445 HOH B 502 SITE 7 AC2 29 HOH B 514 HOH B 569 HOH B 573 HOH B 580 SITE 8 AC2 29 HOH B 639 CRYST1 55.615 74.563 89.952 90.00 98.54 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.017981 0.000000 0.002698 0.00000 SCALE2 0.000000 0.013411 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011242 0.00000