PDB Short entry for 1GD5 HEADER PROTEIN BINDING 14-SEP-00 1GD5 TITLE SOLUTION STRUCTURE OF THE PX DOMAIN FROM HUMAN P47PHOX NADPH OXIDASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUTROPHIL CYTOSOL FACTOR 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PX DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 TISSUE: LYMPHOCYTE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX2T KEYWDS ALPHA BETA, P47-PHOX, PX DOMAIN, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR H.HIROAKI,T.AGO,T.ITO,H.SUMIMOTO,D.KOHDA REVDAT 5 27-DEC-23 1GD5 1 REMARK REVDAT 4 23-FEB-22 1GD5 1 REMARK SEQADV REVDAT 3 24-FEB-09 1GD5 1 VERSN REVDAT 2 28-JAN-03 1GD5 1 REMARK REVDAT 1 13-JUN-01 1GD5 0 JRNL AUTH H.HIROAKI,T.AGO,T.ITO,H.SUMIMOTO,D.KOHDA JRNL TITL SOLUTION STRUCTURE OF THE PX DOMAIN, A TARGET OF THE SH3 JRNL TITL 2 DOMAIN. JRNL REF NAT.STRUCT.BIOL. V. 8 526 2001 JRNL REFN ISSN 1072-8368 JRNL PMID 11373621 JRNL DOI 10.1038/88591 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5, EMBOSS 5.0 REMARK 3 AUTHORS : GUENTERT (DYANA), NAKAMURA (EMBOSS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1GD5 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-OCT-00. REMARK 100 THE DEPOSITION ID IS D_1000005047. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.6MM PX DOMAIN U-15N,13C; 5MM REMARK 210 NA-MES BUFFER; 95% H2O, 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 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 1 LEU A 13 CB - CG - CD2 ANGL. DEV. = 10.9 DEGREES REMARK 500 1 PHE A 52 CB - CG - CD1 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 LEU A 13 CB - CG - CD2 ANGL. DEV. = 10.6 DEGREES REMARK 500 2 PHE A 52 CB - CG - CD1 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 LEU A 96 CB - CG - CD2 ANGL. DEV. = 10.6 DEGREES REMARK 500 3 PHE A 52 CB - CG - CD1 ANGL. DEV. = 5.1 DEGREES REMARK 500 4 LEU A 13 CB - CG - CD2 ANGL. DEV. = 10.4 DEGREES REMARK 500 4 PHE A 52 CB - CG - CD1 ANGL. DEV. = 4.9 DEGREES REMARK 500 5 PHE A 52 CB - CG - CD1 ANGL. DEV. = 5.3 DEGREES REMARK 500 7 PHE A 30 CB - CG - CD1 ANGL. DEV. = 4.3 DEGREES REMARK 500 7 PHE A 52 CB - CG - CD1 ANGL. DEV. = 4.7 DEGREES REMARK 500 7 LEU A 96 CB - CG - CD2 ANGL. DEV. = 10.7 DEGREES REMARK 500 8 LEU A 13 CB - CG - CD2 ANGL. DEV. = 11.4 DEGREES REMARK 500 8 PHE A 52 CB - CG - CD1 ANGL. DEV. = 4.3 DEGREES REMARK 500 9 PHE A 30 CB - CG - CD1 ANGL. DEV. = 5.0 DEGREES REMARK 500 9 PHE A 52 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 9 PHE A 52 CB - CG - CD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 10 TYR A 28 CB - CG - CD1 ANGL. DEV. = -3.6 DEGREES REMARK 500 10 PHE A 30 CB - CG - CD1 ANGL. DEV. = 4.3 DEGREES REMARK 500 10 PHE A 52 CB - CG - CD1 ANGL. DEV. = 5.1 DEGREES REMARK 500 11 ARG A 123 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 13 PHE A 52 CB - CG - CD1 ANGL. DEV. = 4.7 DEGREES REMARK 500 14 PHE A 52 CB - CG - CD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 14 PHE A 52 CB - CG - CD1 ANGL. DEV. = -4.2 DEGREES REMARK 500 15 PHE A 30 CB - CG - CD1 ANGL. DEV. = 4.4 DEGREES REMARK 500 16 PHE A 52 CB - CG - CD1 ANGL. DEV. = 5.0 DEGREES REMARK 500 16 LEU A 96 CB - CG - CD2 ANGL. DEV. = 12.1 DEGREES REMARK 500 17 LEU A 13 CB - CG - CD2 ANGL. DEV. = 10.8 DEGREES REMARK 500 17 PHE A 52 CB - CG - CD1 ANGL. DEV. = 4.8 DEGREES REMARK 500 18 PHE A 52 CB - CG - CD1 ANGL. DEV. = 5.0 DEGREES REMARK 500 19 LEU A 13 CB - CG - CD2 ANGL. DEV. = 10.3 DEGREES REMARK 500 19 PHE A 52 CB - CG - CD1 ANGL. DEV. = 5.3 DEGREES REMARK 500 20 PHE A 52 CB - CG - CD2 ANGL. DEV. = 4.7 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 1 ASP A 5 -43.32 -172.61 REMARK 500 1 THR A 6 -156.47 51.56 REMARK 500 1 ARG A 9 -63.11 -90.00 REMARK 500 1 HIS A 10 -179.62 -175.36 REMARK 500 1 HIS A 25 122.18 -170.93 REMARK 500 1 ASP A 36 -62.58 -125.78 REMARK 500 1 SER A 38 -155.15 69.17 REMARK 500 1 ASN A 71 44.03 -109.62 REMARK 500 1 ARG A 72 54.41 -67.33 REMARK 500 1 ILE A 73 21.79 -143.77 REMARK 500 1 HIS A 76 -139.05 -99.89 REMARK 500 1 LEU A 77 146.12 80.21 REMARK 500 1 LYS A 81 10.88 -149.47 REMARK 500 1 ASP A 84 89.38 -29.81 REMARK 500 1 LEU A 106 132.45 -29.61 REMARK 500 1 THR A 108 43.92 -82.48 REMARK 500 1 ARG A 123 80.91 16.88 REMARK 500 1 ASP A 125 -15.79 -167.05 REMARK 500 1 LEU A 127 20.91 -143.53 REMARK 500 1 LYS A 128 37.94 -149.42 REMARK 500 1 LEU A 129 172.15 -54.20 REMARK 500 2 ASP A 5 -49.09 -163.27 REMARK 500 2 THR A 6 -163.02 45.50 REMARK 500 2 ARG A 9 -63.17 -96.73 REMARK 500 2 HIS A 25 102.58 -165.85 REMARK 500 2 ASP A 36 -64.91 -127.71 REMARK 500 2 SER A 38 -156.28 66.93 REMARK 500 2 HIS A 76 -125.08 -155.22 REMARK 500 2 LEU A 77 151.12 76.62 REMARK 500 2 ASP A 84 85.49 -29.77 REMARK 500 2 LEU A 106 132.53 -32.39 REMARK 500 2 THR A 108 43.63 -83.89 REMARK 500 2 CYS A 113 -73.01 -30.50 REMARK 500 2 PRO A 124 34.64 -71.72 REMARK 500 2 LEU A 127 22.33 -140.58 REMARK 500 2 LYS A 128 32.47 -147.11 REMARK 500 3 ASP A 5 -42.05 179.03 REMARK 500 3 THR A 6 -165.43 48.40 REMARK 500 3 ARG A 9 -62.32 -95.89 REMARK 500 3 HIS A 10 -173.87 -172.65 REMARK 500 3 GLU A 17 163.34 177.67 REMARK 500 3 ASP A 36 -71.21 -133.42 REMARK 500 3 SER A 38 -159.58 68.54 REMARK 500 3 HIS A 76 42.77 -151.67 REMARK 500 3 LYS A 81 30.59 84.82 REMARK 500 3 PHE A 83 47.16 -169.65 REMARK 500 3 ASP A 84 87.31 -29.72 REMARK 500 3 ALA A 89 -62.08 -90.14 REMARK 500 3 LEU A 106 132.26 -29.59 REMARK 500 3 THR A 108 43.36 -84.60 REMARK 500 REMARK 500 THIS ENTRY HAS 356 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 112 0.08 SIDE CHAIN REMARK 500 3 ARG A 44 0.11 SIDE CHAIN REMARK 500 3 ARG A 45 0.10 SIDE CHAIN REMARK 500 6 ARG A 87 0.10 SIDE CHAIN REMARK 500 7 ARG A 44 0.09 SIDE CHAIN REMARK 500 8 ARG A 45 0.11 SIDE CHAIN REMARK 500 9 ARG A 92 0.08 SIDE CHAIN REMARK 500 9 ARG A 123 0.11 SIDE CHAIN REMARK 500 10 ARG A 112 0.08 SIDE CHAIN REMARK 500 12 ARG A 123 0.11 SIDE CHAIN REMARK 500 13 ARG A 87 0.09 SIDE CHAIN REMARK 500 13 ARG A 112 0.09 SIDE CHAIN REMARK 500 14 ARG A 44 0.12 SIDE CHAIN REMARK 500 14 ARG A 45 0.12 SIDE CHAIN REMARK 500 15 ARG A 44 0.12 SIDE CHAIN REMARK 500 18 ARG A 45 0.11 SIDE CHAIN REMARK 500 20 ARG A 19 0.08 SIDE CHAIN REMARK 500 20 ARG A 45 0.10 SIDE CHAIN REMARK 500 20 ARG A 112 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1GD5 A 3 130 UNP P14598 NCF1_HUMAN 1 128 SEQADV 1GD5 GLY A 1 UNP P14598 CLONING ARTIFACT SEQADV 1GD5 SER A 2 UNP P14598 CLONING ARTIFACT SEQRES 1 A 130 GLY SER MET GLY ASP THR PHE ILE ARG HIS ILE ALA LEU SEQRES 2 A 130 LEU GLY PHE GLU LYS ARG PHE VAL PRO SER GLN HIS TYR SEQRES 3 A 130 VAL TYR MET PHE LEU VAL LYS TRP GLN ASP LEU SER GLU SEQRES 4 A 130 LYS VAL VAL TYR ARG ARG PHE THR GLU ILE TYR GLU PHE SEQRES 5 A 130 HIS LYS THR LEU LYS GLU MET PHE PRO ILE GLU ALA GLY SEQRES 6 A 130 ALA ILE ASN PRO GLU ASN ARG ILE ILE PRO HIS LEU PRO SEQRES 7 A 130 ALA PRO LYS TRP PHE ASP GLY GLN ARG ALA ALA GLU ASN SEQRES 8 A 130 ARG GLN GLY THR LEU THR GLU TYR CYS SER THR LEU MET SEQRES 9 A 130 SER LEU PRO THR LYS ILE SER ARG CYS PRO HIS LEU LEU SEQRES 10 A 130 ASP PHE PHE LYS VAL ARG PRO ASP ASP LEU LYS LEU PRO HELIX 1 1 ARG A 45 PHE A 60 1 16 HELIX 2 2 PRO A 61 GLY A 65 5 5 HELIX 3 3 GLY A 85 MET A 104 1 20 HELIX 4 4 ARG A 112 LYS A 121 1 10 SHEET 1 A 3 GLU A 39 ARG A 44 0 SHEET 2 A 3 HIS A 25 TRP A 34 -1 N TYR A 28 O ARG A 44 SHEET 3 A 3 ILE A 8 LEU A 13 -1 N ARG A 9 O LYS A 33 SHEET 1 B 3 GLU A 39 ARG A 44 0 SHEET 2 B 3 HIS A 25 TRP A 34 -1 N TYR A 28 O ARG A 44 SHEET 3 B 3 GLU A 17 ARG A 19 -1 O GLU A 17 N VAL A 27 CISPEP 1 VAL A 21 PRO A 22 1 0.24 CISPEP 2 VAL A 21 PRO A 22 2 0.98 CISPEP 3 VAL A 21 PRO A 22 3 1.05 CISPEP 4 VAL A 21 PRO A 22 4 0.33 CISPEP 5 VAL A 21 PRO A 22 5 0.05 CISPEP 6 VAL A 21 PRO A 22 6 0.89 CISPEP 7 VAL A 21 PRO A 22 7 1.13 CISPEP 8 VAL A 21 PRO A 22 8 0.30 CISPEP 9 VAL A 21 PRO A 22 9 -0.33 CISPEP 10 VAL A 21 PRO A 22 10 1.68 CISPEP 11 VAL A 21 PRO A 22 11 0.57 CISPEP 12 VAL A 21 PRO A 22 12 0.96 CISPEP 13 VAL A 21 PRO A 22 13 0.37 CISPEP 14 VAL A 21 PRO A 22 14 1.07 CISPEP 15 VAL A 21 PRO A 22 15 1.19 CISPEP 16 VAL A 21 PRO A 22 16 0.32 CISPEP 17 VAL A 21 PRO A 22 17 1.09 CISPEP 18 VAL A 21 PRO A 22 18 1.00 CISPEP 19 VAL A 21 PRO A 22 19 1.23 CISPEP 20 VAL A 21 PRO A 22 20 1.12 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000