PDB Short entry for 3IB0 HEADER METAL BINDING PROTEIN 15-JUL-09 3IB0 TITLE STRUCTURAL BASIS OF THE PREVENTION OF NSAID-INDUCED DAMAGE OF THE TITLE 2 GASTROINTESTINAL TRACT BY C-TERMINAL HALF (C-LOBE) OF BOVINE TITLE 3 COLOSTRUM PROTEIN LACTOFERRIN: BINDING AND STRUCTURAL STUDIES OF C- TITLE 4 LOBE COMPLEX WITH DICLOFENAC CAVEAT 3IB0 MAN C 4 HAS WRONG CHIRALITY AT ATOM C1 MAN C 5 HAS WRONG CAVEAT 2 3IB0 CHIRALITY AT ATOM C1 MAN D 4 HAS WRONG CHIRALITY AT ATOM C1 CAVEAT 3 3IB0 MAN D 5 HAS WRONG CHIRALITY AT ATOM C1 MAN D 6 HAS WRONG CAVEAT 4 3IB0 CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LACTOTRANSFERRIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 361-705; COMPND 5 SYNONYM: LACTOFERRIN, LACTOFERRICIN-B, LFCIN-B; COMPND 6 EC: 3.4.21.- SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE; SOURCE 4 ORGANISM_TAXID: 9913 KEYWDS C-LOBE, DRUGS, METAL BINDING PROTEIN, ANTIBIOTIC, ANTIMICROBIAL, KEYWDS 2 DISULFIDE BOND, GLYCOPROTEIN, HYDROLASE, ION TRANSPORT, IRON, IRON KEYWDS 3 TRANSPORT, METAL-BINDING, PHOSPHOPROTEIN, PROTEASE, SECRETED, SERINE KEYWDS 4 PROTEASE, TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR R.MIR,N.SINGH,M.SINHA,S.SHARMA,P.KAUR,A.SRINIVASAN,T.P.SINGH REVDAT 6 29-JUL-20 3IB0 1 CAVEAT COMPND REMARK HETNAM REVDAT 6 2 1 LINK SITE ATOM REVDAT 5 15-AUG-18 3IB0 1 COMPND SOURCE SEQADV REVDAT 4 01-AUG-18 3IB0 1 COMPND SOURCE JRNL REMARK REVDAT 3 13-JUL-11 3IB0 1 VERSN REVDAT 2 09-FEB-10 3IB0 1 JRNL REVDAT 1 11-AUG-09 3IB0 0 SPRSDE 11-AUG-09 3IB0 2B6D 3HWV JRNL AUTH R.MIR,N.SINGH,G.VIKRAM,R.P.KUMAR,M.SINHA,A.BHUSHAN,P.KAUR, JRNL AUTH 2 A.SRINIVASAN,S.SHARMA,T.P.SINGH JRNL TITL THE STRUCTURAL BASIS FOR THE PREVENTION OF NONSTEROIDAL JRNL TITL 2 ANTIINFLAMMATORY DRUG-INDUCED GASTROINTESTINAL TRACT DAMAGE JRNL TITL 3 BY THE C-LOBE OF BOVINE COLOSTRUM LACTOFERRIN JRNL REF BIOPHYS.J. V. 97 3178 2009 JRNL REFN ISSN 0006-3495 JRNL PMID 20006955 JRNL DOI 10.1016/J.BPJ.2009.09.030 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0077 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 62.26 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 70446 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) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3738 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5133 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.86 REMARK 3 BIN R VALUE (WORKING SET) : 0.2910 REMARK 3 BIN FREE R VALUE SET COUNT : 262 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2605 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 200 REMARK 3 SOLVENT ATOMS : 509 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.70000 REMARK 3 B22 (A**2) : -0.63000 REMARK 3 B33 (A**2) : -0.38000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.53000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.070 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.067 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.044 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.107 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2874 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3913 ; 1.467 ; 2.030 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 339 ; 5.216 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 118 ;38.734 ;25.169 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 448 ;13.736 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;16.983 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 463 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2058 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1696 ; 0.635 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2704 ; 1.223 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1178 ; 1.681 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1209 ; 2.829 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 3IB0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000054187. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-SEP-05 REMARK 200 TEMPERATURE (KELVIN) : 203 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70446 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 62.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1NKX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES, 25% POLY ETHYLENE GLYCOL REMARK 280 MONOMETHYL ETHER-550, 0.1M ZNSO4, PH6.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K 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 24.93250 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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, B, C, D 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 THR A 677 REMARK 465 SER A 678 REMARK 465 PRO A 679 REMARK 465 LEU A 680 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 ZN ZN A 689 O HOH A 799 1.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 HIS A 420 CB HIS A 420 CG 0.145 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 HIS A 420 CB - CA - C ANGL. DEV. = -16.2 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 HIS A 420 131.58 -36.91 REMARK 500 ASP A 462 -4.58 81.35 REMARK 500 TRP A 467 -62.30 -144.96 REMARK 500 ALA A 482 49.02 -83.87 REMARK 500 SER A 519 -9.01 -59.01 REMARK 500 VAL A 543 -151.43 -143.42 REMARK 500 SER A 634 30.99 -163.03 REMARK 500 LEU A 640 -47.37 74.07 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 LEU A 681 GLU A 682 -135.46 REMARK 500 GLU A 682 ALA A 683 -135.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 689 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 88 O REMARK 620 2 HIS A 588 NE2 123.0 REMARK 620 3 HOH A 800 O 87.2 91.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 999 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 395 OD1 REMARK 620 2 TYR A 433 OH 87.7 REMARK 620 3 TYR A 526 OH 173.2 95.7 REMARK 620 4 HIS A 595 NE2 93.6 90.1 80.6 REMARK 620 5 CO3 A 687 O1 88.7 156.4 90.5 113.4 REMARK 620 6 CO3 A 687 O2 90.2 93.8 95.4 174.6 62.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 688 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 659 OE1 REMARK 620 2 GLU A 659 OE2 61.0 REMARK 620 3 HOH A 785 O 99.0 93.9 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2B6D RELATED DB: PDB REMARK 900 SPECIFIC BINDING OF NON-STEROIDAL ANTI-INFLAMMATORY DRUGS (NSAIDS) REMARK 900 TO LACTOFERRIN: CRYSTAL STRUCTURE OF THE COMPLEX OF C-TERMINAL LOBE REMARK 900 OF BOVINE LACTOFERRIN WITH DICLOFENAC AT 1.4 A RESOLUTION REMARK 999 REMARK 999 SEQUENCE REMARK 999 NATURAL MUTATIONS HAVE OCCURRED AT 584 ASN AND 627 LYS. DBREF 3IB0 A 342 686 UNP P24627 TRFL_BOVIN 361 705 SEQADV 3IB0 LYS A 565 UNP P24627 ASN 584 SEE SEQUENCE DETAILS SEQADV 3IB0 GLU A 608 UNP P24627 LYS 627 SEE SEQUENCE DETAILS SEQRES 1 A 345 TYR THR ARG VAL VAL TRP CYS ALA VAL GLY PRO GLU GLU SEQRES 2 A 345 GLN LYS LYS CYS GLN GLN TRP SER GLN GLN SER GLY GLN SEQRES 3 A 345 ASN VAL THR CYS ALA THR ALA SER THR THR ASP ASP CYS SEQRES 4 A 345 ILE VAL LEU VAL LEU LYS GLY GLU ALA ASP ALA LEU ASN SEQRES 5 A 345 LEU ASP GLY GLY TYR ILE TYR THR ALA GLY LYS CYS GLY SEQRES 6 A 345 LEU VAL PRO VAL LEU ALA GLU ASN ARG LYS SER SER LYS SEQRES 7 A 345 HIS SER SER LEU ASP CYS VAL LEU ARG PRO THR GLU GLY SEQRES 8 A 345 TYR LEU ALA VAL ALA VAL VAL LYS LYS ALA ASN GLU GLY SEQRES 9 A 345 LEU THR TRP ASN SER LEU LYS ASP LYS LYS SER CYS HIS SEQRES 10 A 345 THR ALA VAL ASP ARG THR ALA GLY TRP ASN ILE PRO MET SEQRES 11 A 345 GLY LEU ILE VAL ASN GLN THR GLY SER CYS ALA PHE ASP SEQRES 12 A 345 GLU PHE PHE SER GLN SER CYS ALA PRO GLY ALA ASP PRO SEQRES 13 A 345 LYS SER ARG LEU CYS ALA LEU CYS ALA GLY ASP ASP GLN SEQRES 14 A 345 GLY LEU ASP LYS CYS VAL PRO ASN SER LYS GLU LYS TYR SEQRES 15 A 345 TYR GLY TYR THR GLY ALA PHE ARG CYS LEU ALA GLU ASP SEQRES 16 A 345 VAL GLY ASP VAL ALA PHE VAL LYS ASN ASP THR VAL TRP SEQRES 17 A 345 GLU ASN THR ASN GLY GLU SER THR ALA ASP TRP ALA LYS SEQRES 18 A 345 ASN LEU LYS ARG GLU ASP PHE ARG LEU LEU CYS LEU ASP SEQRES 19 A 345 GLY THR ARG LYS PRO VAL THR GLU ALA GLN SER CYS HIS SEQRES 20 A 345 LEU ALA VAL ALA PRO ASN HIS ALA VAL VAL SER ARG SER SEQRES 21 A 345 ASP ARG ALA ALA HIS VAL GLU GLN VAL LEU LEU HIS GLN SEQRES 22 A 345 GLN ALA LEU PHE GLY LYS ASN GLY LYS ASN CYS PRO ASP SEQRES 23 A 345 LYS PHE CYS LEU PHE LYS SER GLU THR LYS ASN LEU LEU SEQRES 24 A 345 PHE ASN ASP ASN THR GLU CYS LEU ALA LYS LEU GLY GLY SEQRES 25 A 345 ARG PRO THR TYR GLU GLU TYR LEU GLY THR GLU TYR VAL SEQRES 26 A 345 THR ALA ILE ALA ASN LEU LYS LYS CYS SER THR SER PRO SEQRES 27 A 345 LEU LEU GLU ALA CYS ALA PHE MODRES 3IB0 ASN A 368 ASN GLYCOSYLATION SITE MODRES 3IB0 ASN A 476 ASN GLYCOSYLATION SITE MODRES 3IB0 ASN A 545 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET NAG C 1 14 HET NAG C 2 14 HET MAN C 3 11 HET MAN C 4 11 HET MAN C 5 11 HET NAG D 1 14 HET NAG D 2 14 HET MAN D 3 11 HET MAN D 4 11 HET MAN D 5 11 HET MAN D 6 11 HET FE A 999 1 HET CO3 A 687 4 HET DIF A 701 19 HET SO4 A 1 5 HET SO4 A 2 5 HET ZN A 688 1 HET ZN A 689 1 HET EOH A 703 3 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM FE FE (III) ION HETNAM CO3 CARBONATE ION HETNAM DIF 2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID HETNAM SO4 SULFATE ION HETNAM ZN ZINC ION HETNAM EOH ETHANOL HETSYN DIF DICLOFENAC FORMUL 2 NAG 6(C8 H15 N O6) FORMUL 3 MAN 7(C6 H12 O6) FORMUL 5 FE FE 3+ FORMUL 6 CO3 C O3 2- FORMUL 7 DIF C14 H11 CL2 N O2 FORMUL 8 SO4 2(O4 S 2-) FORMUL 10 ZN 2(ZN 2+) FORMUL 12 EOH C2 H6 O FORMUL 13 HOH *509(H2 O) HELIX 1 1 GLY A 351 SER A 365 1 15 HELIX 2 2 THR A 376 LYS A 386 1 11 HELIX 3 3 ASP A 395 CYS A 405 1 11 HELIX 4 4 ASP A 424 ARG A 428 5 5 HELIX 5 5 THR A 447 LEU A 451 5 5 HELIX 6 6 TRP A 467 GLY A 479 1 13 HELIX 7 7 ALA A 482 PHE A 486 5 5 HELIX 8 8 SER A 499 ALA A 503 5 5 HELIX 9 9 TYR A 524 GLU A 535 1 12 HELIX 10 10 ASN A 545 ASN A 551 1 7 HELIX 11 11 LYS A 565 GLU A 567 5 3 HELIX 12 12 PRO A 580 CYS A 587 5 8 HELIX 13 13 ARG A 600 GLY A 619 1 20 HELIX 14 14 THR A 656 GLY A 662 1 7 HELIX 15 15 GLY A 662 LYS A 674 1 13 SHEET 1 A 2 VAL A 345 VAL A 350 0 SHEET 2 A 2 VAL A 369 ALA A 374 1 O THR A 370 N TRP A 347 SHEET 1 B 4 ALA A 391 LEU A 394 0 SHEET 2 B 4 ALA A 596 SER A 599 -1 O ALA A 596 N LEU A 394 SHEET 3 B 4 VAL A 408 ARG A 415 -1 N VAL A 410 O VAL A 597 SHEET 4 B 4 THR A 645 LYS A 650 -1 O ALA A 649 N ALA A 412 SHEET 1 C 6 GLN A 489 CYS A 491 0 SHEET 2 C 6 LYS A 455 HIS A 458 1 N HIS A 458 O CYS A 491 SHEET 3 C 6 VAL A 540 LYS A 544 1 O PHE A 542 N CYS A 457 SHEET 4 C 6 TYR A 433 LYS A 440 -1 N VAL A 436 O VAL A 543 SHEET 5 C 6 PHE A 569 LEU A 572 -1 O LEU A 572 N ALA A 437 SHEET 6 C 6 ARG A 578 LYS A 579 -1 O LYS A 579 N LEU A 571 SHEET 1 D 5 GLN A 489 CYS A 491 0 SHEET 2 D 5 LYS A 455 HIS A 458 1 N HIS A 458 O CYS A 491 SHEET 3 D 5 VAL A 540 LYS A 544 1 O PHE A 542 N CYS A 457 SHEET 4 D 5 TYR A 433 LYS A 440 -1 N VAL A 436 O VAL A 543 SHEET 5 D 5 ALA A 590 ALA A 592 -1 O ALA A 592 N TYR A 433 SSBOND 1 CYS A 348 CYS A 380 1555 1555 2.04 SSBOND 2 CYS A 358 CYS A 371 1555 1555 2.05 SSBOND 3 CYS A 405 CYS A 684 1555 1555 2.19 SSBOND 4 CYS A 425 CYS A 647 1555 1555 2.04 SSBOND 5 CYS A 457 CYS A 532 1555 1555 2.04 SSBOND 6 CYS A 481 CYS A 675 1555 1555 2.04 SSBOND 7 CYS A 491 CYS A 505 1555 1555 2.05 SSBOND 8 CYS A 502 CYS A 515 1555 1555 1.99 SSBOND 9 CYS A 573 CYS A 587 1555 1555 2.04 SSBOND 10 CYS A 625 CYS A 630 1555 1555 2.05 LINK ND2 ASN A 368 C1 NAG B 1 1555 1555 1.45 LINK ND2 ASN A 476 C1 NAG C 1 1555 1555 1.45 LINK ND2 ASN A 545 C1 NAG D 1 1555 1555 1.44 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.44 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.40 LINK O4 NAG C 2 C1 MAN C 3 1555 1555 1.42 LINK O4 MAN C 3 C1 MAN C 4 1555 1555 1.44 LINK O6 MAN C 3 C1 MAN C 5 1555 1555 1.53 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.43 LINK O4 NAG D 2 C1 MAN D 3 1555 1555 1.48 LINK O4 MAN D 3 C1 MAN D 4 1555 1555 1.46 LINK O4 MAN D 4 C1 MAN D 5 1555 1555 1.50 LINK O4 MAN D 5 C1 MAN D 6 1555 1555 1.44 LINK O HOH A 88 ZN ZN A 689 1555 1555 2.05 LINK OD1 ASP A 395 FE FE A 999 1555 1555 2.16 LINK OH TYR A 433 FE FE A 999 1555 1555 2.01 LINK OH TYR A 526 FE FE A 999 1555 1555 2.04 LINK NE2 HIS A 588 ZN ZN A 689 1555 1555 2.03 LINK NE2 HIS A 595 FE FE A 999 1555 1555 2.13 LINK OE1 GLU A 659 ZN ZN A 688 1555 1555 2.19 LINK OE2 GLU A 659 ZN ZN A 688 1555 1555 2.10 LINK O1 CO3 A 687 FE FE A 999 1555 1555 2.19 LINK O2 CO3 A 687 FE FE A 999 1555 1555 2.10 LINK ZN ZN A 688 O HOH A 785 1555 1555 2.05 LINK ZN ZN A 689 O HOH A 800 1555 1555 2.27 CISPEP 1 CYS A 625 PRO A 626 0 11.40 CRYST1 61.432 49.865 65.165 90.00 107.10 90.00 P 1 21 1 2 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 0.016278 0.000000 0.005008 0.00000 SCALE2 0.000000 0.020054 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016055 0.00000