HEADER HORMONE/GROWTH FACTOR 17-DEC-01 1KMX TITLE HEPARIN-BINDING DOMAIN FROM VASCULAR ENDOTHELIAL GROWTH FACTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HEPARIN-BINDING 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HEPARIN-BINDING, ANGIOGENESIS, GROWTH FACTOR, HORMONE-GROWTH FACTOR KEYWDS 2 COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.E.STAUFFER,N.J.SKELTON,W.J.FAIRBROTHER REVDAT 4 09-OCT-24 1KMX 1 REMARK REVDAT 3 23-FEB-22 1KMX 1 REMARK REVDAT 2 24-FEB-09 1KMX 1 VERSN REVDAT 1 24-JUL-02 1KMX 0 JRNL AUTH M.E.STAUFFER,N.J.SKELTON,W.J.FAIRBROTHER JRNL TITL REFINEMENT OF THE SOLUTION STRUCTURE OF THE HEPARIN-BINDING JRNL TITL 2 DOMAIN OF VASCULAR ENDOTHELIAL GROWTH FACTOR USING RESIDUAL JRNL TITL 3 DIPOLAR COUPLINGS JRNL REF J.BIOMOL.NMR V. 23 57 2002 JRNL REFN ISSN 0925-2738 JRNL PMID 12061718 JRNL DOI 10.1023/A:1015346504499 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH W.J.FAIRBROTHER,M.A.CHAMPE,H.W.CHRISTINGER,B.A.KEYT, REMARK 1 AUTH 2 M.A.STAROVASNIK REMARK 1 TITL SOLUTION STRUCTURE OF THE HEPARIN-BINDING DOMAIN OF VASCULAR REMARK 1 TITL 2 ENDOTHELIAL GROWTH FACTOR REMARK 1 REF STRUCTURE V. 6 637 1998 REMARK 1 REFN ISSN 0969-2126 REMARK 1 DOI 10.1016/S0969-2126(98)00065-3 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : UXNMR, CNX REMARK 3 AUTHORS : MOLECULAR SIMULATIONS, INC. (CNX) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON 459 NOE REMARK 3 -DERIVED DISTANCE RESTRAINTS, 28 H-BOND RESTRAINTS, 66 DIHEDRAL REMARK 3 ANGLE RESTRAINTS, AND 38 RESIDUAL DIPOLAR COUPLING RESTRAINTS REMARK 4 REMARK 4 1KMX COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-DEC-01. REMARK 100 THE DEPOSITION ID IS D_1000015124. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300; 300; 300; 300 REMARK 210 PH : 5.5; 5.5; 5.5; 5.5 REMARK 210 IONIC STRENGTH : 25 MM SODIUM ACETATE; 50 MM REMARK 210 SODIUM CHLORIDE; 25 MM SODIUM REMARK 210 ACETATE; 50 MM SODIUM CHLORIDE; REMARK 210 25 MM SODIUM ACETATE; 50 MM REMARK 210 SODIUM CHLORIDE; 25 MM SODIUM REMARK 210 ACETATE; 50 MM SODIUM CHLORIDE REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT; REMARK 210 AMBIENT REMARK 210 SAMPLE CONTENTS : 2.0 MM VEGF HEPARIN-BINDING REMARK 210 DOMAIN; 25 MM SODIUM ACETATE; 50 REMARK 210 MM SODIUM CHLORIDE, 0.02% SODIUM REMARK 210 AZIDE; 2.0 MM VEGF HEPARIN- REMARK 210 BINDING DOMAIN U-15N; 25 MM REMARK 210 SODIUM ACETATE; 50 MM SODIUM REMARK 210 CHLORIDE, 0.02% SODIUM AZIDE; REMARK 210 2.0 MM VEGF HEPARIN-BINDING REMARK 210 DOMAIN U-15N; 25 MM SODIUM REMARK 210 ACETATE; 50 MM SODIUM CHLORIDE, REMARK 210 0.02% SODIUM AZIDE; 0.6 MM VEGF REMARK 210 HEPARIN-BINDING DOMAIN U-15N; 25 REMARK 210 MM SODIUM ACETATE; 50 MM SODIUM REMARK 210 CHLORIDE; 0.02% SODIUM AZIDE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : DQF-COSY; 2D NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; HNHA; 2D 15N REMARK 210 IPAP-HSQC; 2D 15N IPAP HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AMX; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR, FELIX, CNX REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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 REFINED USING 1H-15N DIPOLAR COUPLING REMARK 210 RESTRAINTS 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-20 REMARK 470 RES CSSEQI ATOMS REMARK 470 ARG A 55 O 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 GLN A 3 -71.95 -160.20 REMARK 500 1 GLU A 4 79.42 68.09 REMARK 500 1 CYS A 10 -71.97 -91.73 REMARK 500 1 SER A 11 -159.16 -90.55 REMARK 500 1 GLU A 12 -70.82 -125.04 REMARK 500 1 ARG A 14 58.72 -94.96 REMARK 500 1 ARG A 54 -69.29 -163.65 REMARK 500 2 ARG A 2 176.17 61.61 REMARK 500 2 PRO A 9 172.32 -45.43 REMARK 500 2 CYS A 10 -82.83 -90.31 REMARK 500 2 ARG A 13 -59.40 -127.76 REMARK 500 2 ARG A 14 59.22 -90.60 REMARK 500 2 ARG A 54 -48.35 -159.83 REMARK 500 3 PRO A 9 174.85 -56.61 REMARK 500 3 CYS A 10 -79.70 -90.10 REMARK 500 3 ARG A 13 -71.49 -141.76 REMARK 500 3 ARG A 14 45.22 -158.46 REMARK 500 3 HIS A 16 -46.36 -161.16 REMARK 500 3 PRO A 22 39.40 -89.68 REMARK 500 3 GLN A 23 -49.24 -148.82 REMARK 500 3 PRO A 53 -75.09 -85.48 REMARK 500 3 ARG A 54 -140.42 -154.53 REMARK 500 4 ARG A 2 -166.23 60.72 REMARK 500 4 GLN A 3 73.61 58.72 REMARK 500 4 GLU A 4 33.98 -141.21 REMARK 500 4 ARG A 14 83.51 -67.84 REMARK 500 4 LYS A 15 176.55 -41.52 REMARK 500 4 HIS A 16 -48.14 -153.68 REMARK 500 4 ARG A 54 -92.12 -159.14 REMARK 500 5 ARG A 2 -159.57 -89.56 REMARK 500 5 GLU A 4 112.39 64.98 REMARK 500 5 ASN A 5 85.63 -150.21 REMARK 500 5 PRO A 9 178.84 -47.97 REMARK 500 5 CYS A 10 -93.65 -90.08 REMARK 500 5 GLU A 12 32.17 -141.82 REMARK 500 5 ARG A 13 -43.69 -150.49 REMARK 500 5 ARG A 14 60.58 -152.61 REMARK 500 5 LEU A 17 44.70 -97.08 REMARK 500 5 ARG A 54 -54.54 -139.16 REMARK 500 6 CYS A 10 -64.83 -90.37 REMARK 500 6 ARG A 13 -46.90 -138.71 REMARK 500 6 ARG A 14 59.07 -93.47 REMARK 500 6 ARG A 54 -69.51 -142.42 REMARK 500 7 ARG A 2 -45.58 -159.28 REMARK 500 7 PRO A 6 -156.45 -58.15 REMARK 500 7 PRO A 9 -169.45 -72.45 REMARK 500 7 CYS A 10 -76.16 -88.67 REMARK 500 7 SER A 11 -76.80 -88.48 REMARK 500 7 GLU A 12 -67.21 -156.97 REMARK 500 7 ARG A 13 -48.44 -142.36 REMARK 500 REMARK 500 THIS ENTRY HAS 152 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1VGH RELATED DB: PDB REMARK 900 1VGH IS THE SAME PROTEIN BUT REFINED WITHOUT USING RESIDUAL DIPOLAR REMARK 900 COUPLING RESTRAINTS REMARK 900 RELATED ID: 2VGH RELATED DB: PDB REMARK 900 2VGH IS THE MINIMIZED MEAN CORRESPONDING THE THE SAME PROTEIN REMARK 900 REFINED WITHOUT RESIDUAL DIPOLAR COUPLING RESTRAINTS DBREF 1KMX A 1 55 UNP P15692 VEGFA_HUMAN 137 191 SEQRES 1 A 55 ALA ARG GLN GLU ASN PRO CYS GLY PRO CYS SER GLU ARG SEQRES 2 A 55 ARG LYS HIS LEU PHE VAL GLN ASP PRO GLN THR CYS LYS SEQRES 3 A 55 CYS SER CYS LYS ASN THR ASP SER ARG CYS LYS ALA ARG SEQRES 4 A 55 GLN LEU GLU LEU ASN GLU ARG THR CYS ARG CYS ASP LYS SEQRES 5 A 55 PRO ARG ARG HELIX 1 1 THR A 32 ALA A 38 1 7 SHEET 1 A 2 PHE A 18 GLN A 20 0 SHEET 2 A 2 CYS A 27 CYS A 29 -1 O SER A 28 N VAL A 19 SHEET 1 B 2 GLU A 42 ASN A 44 0 SHEET 2 B 2 ARG A 49 ASP A 51 -1 O ARG A 49 N ASN A 44 SSBOND 1 CYS A 7 CYS A 25 1555 1555 2.03 SSBOND 2 CYS A 10 CYS A 27 1555 1555 2.03 SSBOND 3 CYS A 29 CYS A 48 1555 1555 2.03 SSBOND 4 CYS A 36 CYS A 50 1555 1555 2.03 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 MODEL 1