HEADER SIGNALING PROTEIN 08-NOV-19 6TDB TITLE NEUROPILIN2-B1 DOMAIN IN A COMPLEX WITH THE C-TERMINAL VEGFB167 TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROPILIN-2; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: VASCULAR ENDOTHELIAL CELL GROWTH FACTOR 165 RECEPTOR 2; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: THE FIRST N TERMINAL RESIDUE IN CHAINS B, C AND D, THE COMPND 7 FOUR C TERMINAL RESIDUES IN CHAIN A, B AND C, AND THE TWO C TERMINAL COMPND 8 RESIDUES IN CHAIN D, WERE NOT SEEN IN AN ELECTRON DENSITY MAP.; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: C-TERMINAL VEGFB167 PEPTIDE; COMPND 11 CHAIN: F, J, K; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: THE ELECTRON DENSITY FOR THIS PEPTIDE ONLY ALLOWS FOR COMPND 14 MODELLING OF TWO C TERMINAL RESIDUES. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NRP2, VEGF165R2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS VEGF-BINDING, NRP2, ANGIOGENESIS, IMMUNOMODULATION, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.ELDRID,L.YU,T.YELLAND,C.FOTINOU,S.DJORDJEVIC REVDAT 2 24-JAN-24 6TDB 1 REMARK REVDAT 1 18-NOV-20 6TDB 0 JRNL AUTH C.ELDRID,L.YU,T.YELLAND,C.FOTINOU,S.DJORDJEVIC JRNL TITL NRP2-B1 DOMAIN IN A COMPLEX WITH THE C-TERMINAL VEGFB167 JRNL TITL 2 PEPTIDE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.V.AFONINE,R.W.GROSSE-KUNSTLEVE,N.ECHOLS,J.J.HEADD, REMARK 1 AUTH 2 N.W.MORIARTY,M.MUSTYAKIMOV,T.C.TERWILLIGER,A.URZHUMTSEV, REMARK 1 AUTH 3 P.H.ZWART,P.D.ADAMS REMARK 1 TITL TOWARDS AUTOMATED CRYSTALLOGRAPHIC STRUCTURE REFINEMENT WITH REMARK 1 TITL 2 PHENIX.REFINE. REMARK 1 REF ACTA CRYSTALLOGR. D BIOL. V. 68 352 2012 REMARK 1 REF 2 CRYSTALLOGR. REMARK 1 REFN ESSN 1399-0047 REMARK 1 PMID 22505256 REMARK 1 DOI 10.1107/S0907444912001308 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 70.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 29159 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1428 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 70.0600 - 5.2800 0.97 2746 146 0.1802 0.2151 REMARK 3 2 5.2800 - 4.1900 0.98 2780 124 0.1433 0.2106 REMARK 3 3 4.1900 - 3.6600 0.98 2746 148 0.1646 0.2010 REMARK 3 4 3.6600 - 3.3300 0.99 2815 120 0.1753 0.2769 REMARK 3 5 3.3300 - 3.0900 1.00 2793 128 0.1880 0.2829 REMARK 3 6 3.0900 - 2.9100 0.99 2787 139 0.2053 0.2936 REMARK 3 7 2.9100 - 2.7600 0.99 2767 141 0.2292 0.2998 REMARK 3 8 2.7600 - 2.6400 0.99 2794 139 0.2414 0.3423 REMARK 3 9 2.6400 - 2.5400 1.00 2747 177 0.2537 0.3355 REMARK 3 10 2.5400 - 2.4500 1.00 2756 166 0.2532 0.3143 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.362 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.264 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 5291 REMARK 3 ANGLE : 0.691 7170 REMARK 3 CHIRALITY : 0.047 767 REMARK 3 PLANARITY : 0.003 938 REMARK 3 DIHEDRAL : 21.023 1948 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6TDB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1292105286. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JAN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.977 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29170 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 70.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.58 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 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: PHASER REMARK 200 STARTING MODEL: 4RN5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: N2B1-APO 0.05 M KCL, 0.01 M MGCL2 AND REMARK 280 15 % (W/V) PEG600 N2B1/VEGFB167 0.1 M HEPES PH 7.5, 10 % (W/V) REMARK 280 PEG4000, 20 % (W/V) ISOPROPANOL, VAPOR DIFFUSION, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 53.67950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 70.06100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 53.67950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 70.06100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, F 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, F 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: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, J 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: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, K 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH D 555 LIES ON A SPECIAL POSITION. 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 430 REMARK 465 SER A 431 REMARK 465 GLY A 432 REMARK 465 SER A 433 REMARK 465 GLY B 272 REMARK 465 THR B 430 REMARK 465 SER B 431 REMARK 465 GLY B 432 REMARK 465 SER B 433 REMARK 465 GLY C 272 REMARK 465 THR C 430 REMARK 465 SER C 431 REMARK 465 GLY C 432 REMARK 465 SER C 433 REMARK 465 GLY D 272 REMARK 465 GLY D 432 REMARK 465 SER D 433 REMARK 465 ARG J 228 REMARK 465 LYS J 229 REMARK 465 LEU J 230 REMARK 465 ARG K 228 REMARK 465 LYS K 229 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 LYS B 379 CE NZ REMARK 470 ARG B 428 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 287 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 379 CG CD CE NZ REMARK 470 VAL C 429 CG1 CG2 REMARK 470 ARG D 287 NE CZ NH1 NH2 REMARK 470 ASP D 314 CG OD1 OD2 REMARK 470 LEU D 322 CG CD1 CD2 REMARK 470 LYS D 326 CD CE NZ REMARK 470 GLU D 351 CG CD OE1 OE2 REMARK 470 LYS D 379 CG CD CE NZ REMARK 470 VAL D 429 CG1 CG2 REMARK 470 ARG J 231 CG CD NE CZ NH1 NH2 REMARK 470 LEU K 230 CG CD1 CD2 REMARK 470 ARG K 231 CD NE CZ NH1 NH2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 MET A 338 CG 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 278 26.56 -167.59 REMARK 500 GLU A 284 -56.42 73.39 REMARK 500 SER A 285 -79.45 -55.52 REMARK 500 TRP A 304 48.19 -140.11 REMARK 500 ASN A 316 -145.04 52.05 REMARK 500 ARG A 334 -16.71 74.16 REMARK 500 GLN A 353 19.21 54.83 REMARK 500 ALA A 386 -118.67 -121.25 REMARK 500 SER A 416 -57.69 76.72 REMARK 500 ASN B 278 23.60 -160.52 REMARK 500 SER B 297 -177.57 -177.88 REMARK 500 ASN B 316 -141.20 62.42 REMARK 500 ARG B 334 -35.14 80.29 REMARK 500 ALA B 386 -132.58 -118.59 REMARK 500 SER B 416 -33.37 61.10 REMARK 500 CYS B 427 138.59 -178.18 REMARK 500 ASN C 278 28.11 -161.48 REMARK 500 ASP C 301 11.00 -68.66 REMARK 500 ASN C 316 -147.71 53.64 REMARK 500 ARG C 334 -17.86 64.92 REMARK 500 ALA C 386 -126.39 -106.24 REMARK 500 ASP C 389 -164.51 -126.50 REMARK 500 SER C 416 -6.26 70.99 REMARK 500 CYS C 427 149.54 -171.19 REMARK 500 ASN D 278 29.65 -162.82 REMARK 500 ASN D 316 -135.87 62.82 REMARK 500 ARG D 334 -41.67 74.88 REMARK 500 ALA D 386 -128.91 -124.88 REMARK 500 ALA D 400 142.96 -173.53 REMARK 500 SER D 416 -50.95 68.78 REMARK 500 THR D 430 -154.72 -133.19 REMARK 500 LYS F 229 95.92 57.29 REMARK 500 ARG K 231 100.11 59.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 685 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A 686 DISTANCE = 6.69 ANGSTROMS REMARK 525 HOH A 687 DISTANCE = 7.39 ANGSTROMS REMARK 525 HOH B 680 DISTANCE = 6.39 ANGSTROMS REMARK 525 HOH B 681 DISTANCE = 6.62 ANGSTROMS REMARK 525 HOH B 682 DISTANCE = 6.79 ANGSTROMS REMARK 525 HOH B 683 DISTANCE = 7.19 ANGSTROMS REMARK 525 HOH B 684 DISTANCE = 7.42 ANGSTROMS REMARK 525 HOH C 646 DISTANCE = 10.85 ANGSTROMS REMARK 525 HOH C 647 DISTANCE = 12.98 ANGSTROMS REMARK 525 HOH D 551 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH D 552 DISTANCE = 6.73 ANGSTROMS REMARK 525 HOH D 553 DISTANCE = 6.89 ANGSTROMS REMARK 525 HOH D 554 DISTANCE = 8.65 ANGSTROMS REMARK 525 HOH D 555 DISTANCE = 12.54 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide ACE F 301 and ARG F REMARK 800 228 DBREF 6TDB A 275 430 UNP O60462 NRP2_HUMAN 275 430 DBREF 6TDB B 275 430 UNP O60462 NRP2_HUMAN 275 430 DBREF 6TDB C 275 430 UNP O60462 NRP2_HUMAN 275 430 DBREF 6TDB D 275 430 UNP O60462 NRP2_HUMAN 275 430 DBREF 6TDB F 228 232 PDB 6TDB 6TDB 228 232 DBREF 6TDB J 228 232 PDB 6TDB 6TDB 228 232 DBREF 6TDB K 228 232 PDB 6TDB 6TDB 228 232 SEQADV 6TDB GLY A 272 UNP O60462 EXPRESSION TAG SEQADV 6TDB HIS A 273 UNP O60462 EXPRESSION TAG SEQADV 6TDB MET A 274 UNP O60462 EXPRESSION TAG SEQADV 6TDB SER A 431 UNP O60462 EXPRESSION TAG SEQADV 6TDB GLY A 432 UNP O60462 EXPRESSION TAG SEQADV 6TDB SER A 433 UNP O60462 EXPRESSION TAG SEQADV 6TDB GLY B 272 UNP O60462 EXPRESSION TAG SEQADV 6TDB HIS B 273 UNP O60462 EXPRESSION TAG SEQADV 6TDB MET B 274 UNP O60462 EXPRESSION TAG SEQADV 6TDB SER B 431 UNP O60462 EXPRESSION TAG SEQADV 6TDB GLY B 432 UNP O60462 EXPRESSION TAG SEQADV 6TDB SER B 433 UNP O60462 EXPRESSION TAG SEQADV 6TDB GLY C 272 UNP O60462 EXPRESSION TAG SEQADV 6TDB HIS C 273 UNP O60462 EXPRESSION TAG SEQADV 6TDB MET C 274 UNP O60462 EXPRESSION TAG SEQADV 6TDB SER C 431 UNP O60462 EXPRESSION TAG SEQADV 6TDB GLY C 432 UNP O60462 EXPRESSION TAG SEQADV 6TDB SER C 433 UNP O60462 EXPRESSION TAG SEQADV 6TDB GLY D 272 UNP O60462 EXPRESSION TAG SEQADV 6TDB HIS D 273 UNP O60462 EXPRESSION TAG SEQADV 6TDB MET D 274 UNP O60462 EXPRESSION TAG SEQADV 6TDB SER D 431 UNP O60462 EXPRESSION TAG SEQADV 6TDB GLY D 432 UNP O60462 EXPRESSION TAG SEQADV 6TDB SER D 433 UNP O60462 EXPRESSION TAG SEQRES 1 A 162 GLY HIS MET PHE GLN CYS ASN VAL PRO LEU GLY MET GLU SEQRES 2 A 162 SER GLY ARG ILE ALA ASN GLU GLN ILE SER ALA SER SER SEQRES 3 A 162 THR TYR SER ASP GLY ARG TRP THR PRO GLN GLN SER ARG SEQRES 4 A 162 LEU HIS GLY ASP ASP ASN GLY TRP THR PRO ASN LEU ASP SEQRES 5 A 162 SER ASN LYS GLU TYR LEU GLN VAL ASP LEU ARG PHE LEU SEQRES 6 A 162 THR MET LEU THR ALA ILE ALA THR GLN GLY ALA ILE SER SEQRES 7 A 162 ARG GLU THR GLN ASN GLY TYR TYR VAL LYS SER TYR LYS SEQRES 8 A 162 LEU GLU VAL SER THR ASN GLY GLU ASP TRP MET VAL TYR SEQRES 9 A 162 ARG HIS GLY LYS ASN HIS LYS VAL PHE GLN ALA ASN ASN SEQRES 10 A 162 ASP ALA THR GLU VAL VAL LEU ASN LYS LEU HIS ALA PRO SEQRES 11 A 162 LEU LEU THR ARG PHE VAL ARG ILE ARG PRO GLN THR TRP SEQRES 12 A 162 HIS SER GLY ILE ALA LEU ARG LEU GLU LEU PHE GLY CYS SEQRES 13 A 162 ARG VAL THR SER GLY SER SEQRES 1 B 162 GLY HIS MET PHE GLN CYS ASN VAL PRO LEU GLY MET GLU SEQRES 2 B 162 SER GLY ARG ILE ALA ASN GLU GLN ILE SER ALA SER SER SEQRES 3 B 162 THR TYR SER ASP GLY ARG TRP THR PRO GLN GLN SER ARG SEQRES 4 B 162 LEU HIS GLY ASP ASP ASN GLY TRP THR PRO ASN LEU ASP SEQRES 5 B 162 SER ASN LYS GLU TYR LEU GLN VAL ASP LEU ARG PHE LEU SEQRES 6 B 162 THR MET LEU THR ALA ILE ALA THR GLN GLY ALA ILE SER SEQRES 7 B 162 ARG GLU THR GLN ASN GLY TYR TYR VAL LYS SER TYR LYS SEQRES 8 B 162 LEU GLU VAL SER THR ASN GLY GLU ASP TRP MET VAL TYR SEQRES 9 B 162 ARG HIS GLY LYS ASN HIS LYS VAL PHE GLN ALA ASN ASN SEQRES 10 B 162 ASP ALA THR GLU VAL VAL LEU ASN LYS LEU HIS ALA PRO SEQRES 11 B 162 LEU LEU THR ARG PHE VAL ARG ILE ARG PRO GLN THR TRP SEQRES 12 B 162 HIS SER GLY ILE ALA LEU ARG LEU GLU LEU PHE GLY CYS SEQRES 13 B 162 ARG VAL THR SER GLY SER SEQRES 1 C 162 GLY HIS MET PHE GLN CYS ASN VAL PRO LEU GLY MET GLU SEQRES 2 C 162 SER GLY ARG ILE ALA ASN GLU GLN ILE SER ALA SER SER SEQRES 3 C 162 THR TYR SER ASP GLY ARG TRP THR PRO GLN GLN SER ARG SEQRES 4 C 162 LEU HIS GLY ASP ASP ASN GLY TRP THR PRO ASN LEU ASP SEQRES 5 C 162 SER ASN LYS GLU TYR LEU GLN VAL ASP LEU ARG PHE LEU SEQRES 6 C 162 THR MET LEU THR ALA ILE ALA THR GLN GLY ALA ILE SER SEQRES 7 C 162 ARG GLU THR GLN ASN GLY TYR TYR VAL LYS SER TYR LYS SEQRES 8 C 162 LEU GLU VAL SER THR ASN GLY GLU ASP TRP MET VAL TYR SEQRES 9 C 162 ARG HIS GLY LYS ASN HIS LYS VAL PHE GLN ALA ASN ASN SEQRES 10 C 162 ASP ALA THR GLU VAL VAL LEU ASN LYS LEU HIS ALA PRO SEQRES 11 C 162 LEU LEU THR ARG PHE VAL ARG ILE ARG PRO GLN THR TRP SEQRES 12 C 162 HIS SER GLY ILE ALA LEU ARG LEU GLU LEU PHE GLY CYS SEQRES 13 C 162 ARG VAL THR SER GLY SER SEQRES 1 D 162 GLY HIS MET PHE GLN CYS ASN VAL PRO LEU GLY MET GLU SEQRES 2 D 162 SER GLY ARG ILE ALA ASN GLU GLN ILE SER ALA SER SER SEQRES 3 D 162 THR TYR SER ASP GLY ARG TRP THR PRO GLN GLN SER ARG SEQRES 4 D 162 LEU HIS GLY ASP ASP ASN GLY TRP THR PRO ASN LEU ASP SEQRES 5 D 162 SER ASN LYS GLU TYR LEU GLN VAL ASP LEU ARG PHE LEU SEQRES 6 D 162 THR MET LEU THR ALA ILE ALA THR GLN GLY ALA ILE SER SEQRES 7 D 162 ARG GLU THR GLN ASN GLY TYR TYR VAL LYS SER TYR LYS SEQRES 8 D 162 LEU GLU VAL SER THR ASN GLY GLU ASP TRP MET VAL TYR SEQRES 9 D 162 ARG HIS GLY LYS ASN HIS LYS VAL PHE GLN ALA ASN ASN SEQRES 10 D 162 ASP ALA THR GLU VAL VAL LEU ASN LYS LEU HIS ALA PRO SEQRES 11 D 162 LEU LEU THR ARG PHE VAL ARG ILE ARG PRO GLN THR TRP SEQRES 12 D 162 HIS SER GLY ILE ALA LEU ARG LEU GLU LEU PHE GLY CYS SEQRES 13 D 162 ARG VAL THR SER GLY SER SEQRES 1 F 5 ARG LYS LEU ARG ARG SEQRES 1 J 5 ARG LYS LEU ARG ARG SEQRES 1 K 5 ARG LYS LEU ARG ARG HET EDO A 501 10 HET EDO B 501 10 HET EDO C 501 10 HET ACE F 301 3 HETNAM EDO 1,2-ETHANEDIOL HETNAM ACE ACETYL GROUP HETSYN EDO ETHYLENE GLYCOL FORMUL 8 EDO 3(C2 H6 O2) FORMUL 11 ACE C2 H4 O FORMUL 12 HOH *277(H2 O) HELIX 1 1 ASN A 290 GLN A 292 5 3 HELIX 2 2 PRO A 306 GLN A 308 5 3 HELIX 3 3 ASN B 290 GLN B 292 5 3 HELIX 4 4 PRO B 306 GLN B 308 5 3 HELIX 5 5 ASN C 290 GLN C 292 5 3 HELIX 6 6 PRO C 306 GLN C 308 5 3 HELIX 7 7 ASN D 290 GLN D 292 5 3 HELIX 8 8 PRO D 306 GLN D 308 5 3 SHEET 1 A 4 ILE A 293 ALA A 295 0 SHEET 2 A 4 LEU A 329 ASP A 332 -1 SHEET 3 A 4 PHE A 406 PRO A 411 -1 SHEET 4 A 4 TYR A 361 SER A 366 -1 SHEET 1 B 3 LEU A 402 THR A 404 0 SHEET 2 B 3 THR A 337 GLN A 345 -1 SHEET 3 B 3 ARG A 421 ARG A 428 -1 SHEET 1 C 2 ALA A 341 THR A 344 0 SHEET 2 C 2 VAL A 394 LYS A 397 -1 SHEET 1 D 2 TYR A 357 SER A 360 0 SHEET 2 D 2 THR A 413 HIS A 415 -1 SHEET 1 E 4 ILE B 293 ALA B 295 0 SHEET 2 E 4 LEU B 329 ASP B 332 -1 SHEET 3 E 4 PHE B 406 PRO B 411 -1 SHEET 4 E 4 TYR B 361 SER B 366 -1 SHEET 1 F 3 LEU B 402 THR B 404 0 SHEET 2 F 3 THR B 337 GLN B 345 -1 SHEET 3 F 3 ARG B 421 ARG B 428 -1 SHEET 1 G 2 ALA B 341 THR B 344 0 SHEET 2 G 2 VAL B 394 LYS B 397 -1 SHEET 1 H 2 TYR B 357 SER B 360 0 SHEET 2 H 2 THR B 413 HIS B 415 -1 SHEET 1 I 5 ILE C 293 ALA C 295 0 SHEET 2 I 5 LEU C 329 ASP C 332 -1 SHEET 3 I 5 PHE C 406 PRO C 411 -1 SHEET 4 I 5 SER C 360 SER C 366 -1 SHEET 5 I 5 VAL C 383 GLN C 385 -1 SHEET 1 J 3 LEU C 402 THR C 404 0 SHEET 2 J 3 THR C 337 GLN C 345 -1 SHEET 3 J 3 ARG C 421 ARG C 428 -1 SHEET 1 K 2 ALA C 341 THR C 344 0 SHEET 2 K 2 VAL C 394 LYS C 397 -1 SHEET 1 L 2 TYR C 357 SER C 360 0 SHEET 2 L 2 THR C 413 HIS C 415 -1 SHEET 1 M 4 ILE D 293 ALA D 295 0 SHEET 2 M 4 LEU D 329 ASP D 332 -1 SHEET 3 M 4 PHE D 406 PRO D 411 -1 SHEET 4 M 4 TYR D 361 SER D 366 -1 SHEET 1 N 3 LEU D 402 THR D 404 0 SHEET 2 N 3 THR D 337 GLN D 345 -1 SHEET 3 N 3 ARG D 421 ARG D 428 -1 SHEET 1 O 2 ALA D 341 THR D 344 0 SHEET 2 O 2 VAL D 394 LYS D 397 -1 SHEET 1 P 2 TYR D 357 SER D 360 0 SHEET 2 P 2 THR D 413 HIS D 415 -1 SSBOND 1 CYS A 277 CYS A 427 1555 1555 2.03 SSBOND 2 CYS B 277 CYS B 427 1555 1555 2.03 SSBOND 3 CYS C 277 CYS C 427 1555 1555 2.03 SSBOND 4 CYS D 277 CYS D 427 1555 1555 2.03 LINK N ARG F 228 C ACE F 301 1555 1555 1.34 SITE 1 AC1 5 LYS A 382 GLN A 385 ASN A 388 ASP A 389 SITE 2 AC1 5 ASN A 396 SITE 1 AC2 5 GLY B 313 ASN B 316 ALA B 347 ILE B 348 SITE 2 AC2 5 ARG B 421 SITE 1 AC3 3 ASN C 278 THR C 340 ALA C 341 SITE 1 AC4 8 ASP B 301 TRP B 304 THR B 319 SER B 349 SITE 2 AC4 8 GLU B 351 TYR B 356 ILE B 418 LYS F 229 CRYST1 107.359 140.122 74.357 90.00 132.97 90.00 C 1 2 1 16 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 0.009315 0.000000 0.008677 0.00000 SCALE2 0.000000 0.007137 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018380 0.00000