HEADER TRANSFERASE 11-NOV-20 7KPM TITLE CRYSTAL STRUCTURE OF HEPHB1 BOUND WITH ADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: EPHRIN TYPE-B RECEPTOR 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ELK,EPH TYROSINE KINASE 2,EPH-LIKE KINASE 6,HEK6,NEURONALLY- COMPND 5 EXPRESSED EPH-RELATED TYROSINE KINASE,NET,TYROSINE-PROTEIN KINASE COMPND 6 RECEPTOR EPH-2; COMPND 7 EC: 2.7.10.1; 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: EPHB1, ELK, EPHT2, HEK6, NET; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HEPHB1, ADP, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.AHMED,P.WANG,H.SADEK REVDAT 4 23-OCT-24 7KPM 1 REMARK REVDAT 3 15-NOV-23 7KPM 1 REMARK REVDAT 2 18-OCT-23 7KPM 1 REMARK REVDAT 1 10-MAR-21 7KPM 0 JRNL AUTH M.S.AHMED,P.WANG,N.U.N.NGUYEN,Y.NAKADA,I.MENENDEZ-MONTES, JRNL AUTH 2 M.ISMAIL,R.BACHOO,M.HENKEMEYER,H.A.SADEK,E.S.KANDIL JRNL TITL IDENTIFICATION OF TETRACYCLINE COMBINATIONS AS EPHB1 JRNL TITL 2 TYROSINE KINASE INHIBITORS FOR TREATMENT OF NEUROPATHIC JRNL TITL 3 PAIN. JRNL REF PROC.NATL.ACAD.SCI.USA V. 118 2021 JRNL REFN ESSN 1091-6490 JRNL PMID 33627480 JRNL DOI 10.1073/PNAS.2016265118 REMARK 2 REMARK 2 RESOLUTION. 1.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 37926 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 1869 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 48.4550 - 3.7793 0.98 3022 142 0.1698 0.1928 REMARK 3 2 3.7793 - 2.9999 1.00 2896 173 0.1613 0.1800 REMARK 3 3 2.9999 - 2.6207 0.99 2862 140 0.1720 0.2128 REMARK 3 4 2.6207 - 2.3811 0.99 2881 113 0.1663 0.1926 REMARK 3 5 2.3811 - 2.2104 1.00 2833 148 0.1604 0.1878 REMARK 3 6 2.2104 - 2.0801 0.99 2836 143 0.1499 0.1924 REMARK 3 7 2.0801 - 1.9759 0.99 2817 158 0.1555 0.1904 REMARK 3 8 1.9759 - 1.8899 1.00 2829 156 0.1612 0.1966 REMARK 3 9 1.8899 - 1.8172 0.99 2819 148 0.1701 0.2199 REMARK 3 10 1.8172 - 1.7545 0.98 2742 153 0.1737 0.2121 REMARK 3 11 1.7545 - 1.6996 0.96 2728 150 0.1868 0.2386 REMARK 3 12 1.6996 - 1.6510 0.95 2647 133 0.1955 0.2133 REMARK 3 13 1.6510 - 1.6080 0.75 2145 112 0.2022 0.2357 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.670 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.85 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 14.1937 -8.2937 -18.9093 REMARK 3 T TENSOR REMARK 3 T11: 0.0596 T22: 0.0693 REMARK 3 T33: 0.0857 T12: 0.0094 REMARK 3 T13: -0.0023 T23: 0.0081 REMARK 3 L TENSOR REMARK 3 L11: 0.2762 L22: 0.3847 REMARK 3 L33: 1.1022 L12: 0.0125 REMARK 3 L13: -0.2108 L23: 0.1764 REMARK 3 S TENSOR REMARK 3 S11: -0.0109 S12: 0.0460 S13: 0.0079 REMARK 3 S21: -0.0298 S22: -0.0287 S23: 0.0281 REMARK 3 S31: 0.0620 S32: -0.0399 S33: 0.0312 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 7KPM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1000252910. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-NOV-20 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 : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38492 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : 0.25000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.55000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 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: PDB ENTRY 3ZFX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM MALONATE, PH 4.6, 14% REMARK 280 PEG3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 16.56700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.45500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.68100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.45500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.56700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.68100 REMARK 290 SMTRY3 4 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 TOTAL BURIED SURFACE AREA: 760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL 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 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 764 REMARK 465 LEU A 765 REMARK 465 SER A 766 REMARK 465 ARG A 767 REMARK 465 TYR A 768 REMARK 465 LEU A 769 REMARK 465 GLN A 770 REMARK 465 ASP A 771 REMARK 465 ASP A 772 REMARK 465 THR A 773 REMARK 465 SER A 774 REMARK 465 ASP A 775 REMARK 465 PRO A 776 REMARK 465 THR A 777 REMARK 465 TYR A 778 REMARK 465 THR A 779 REMARK 465 SER A 780 REMARK 465 SER A 781 REMARK 465 LEU A 782 REMARK 465 GLY A 783 REMARK 465 GLY A 784 REMARK 465 LYS A 785 REMARK 465 ILE A 786 REMARK 465 LYS A 889 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 GLU A 622 -135.21 -118.50 REMARK 500 ASP A 676 89.48 -150.24 REMARK 500 ARG A 743 -13.35 75.58 REMARK 500 SER A 761 -161.15 -129.01 REMARK 500 TRP A 826 -122.71 49.72 REMARK 500 REMARK 500 REMARK: NULL DBREF 7KPM A 611 889 UNP P54762 EPHB1_HUMAN 172 450 SEQRES 1 A 279 ALA LYS GLU ILE ASP VAL SER PHE VAL LYS ILE GLU GLU SEQRES 2 A 279 VAL ILE GLY ALA GLY GLU PHE GLY GLU VAL TYR LYS GLY SEQRES 3 A 279 ARG LEU LYS LEU PRO GLY LYS ARG GLU ILE PTR VAL ALA SEQRES 4 A 279 ILE LYS THR LEU LYS ALA GLY TYR SER GLU LYS GLN ARG SEQRES 5 A 279 ARG ASP PHE LEU SER GLU ALA SER ILE MET GLY GLN PHE SEQRES 6 A 279 ASP HIS PRO ASN ILE ILE ARG LEU GLU GLY VAL VAL THR SEQRES 7 A 279 LYS SER ARG PRO VAL MET ILE ILE THR GLU PHE MET GLU SEQRES 8 A 279 ASN GLY ALA LEU ASP SER PHE LEU ARG GLN ASN ASP GLY SEQRES 9 A 279 GLN PHE THR VAL ILE GLN LEU VAL GLY MET LEU ARG GLY SEQRES 10 A 279 ILE ALA ALA GLY MET LYS TYR LEU ALA GLU MET ASN TYR SEQRES 11 A 279 VAL HIS ARG ASP LEU ALA ALA ARG ASN ILE LEU VAL ASN SEQRES 12 A 279 SER ASN LEU VAL CYS LYS VAL SER ASP PHE GLY LEU SER SEQRES 13 A 279 ARG TYR LEU GLN ASP ASP THR SER ASP PRO THR TYR THR SEQRES 14 A 279 SER SER LEU GLY GLY LYS ILE PRO VAL ARG TRP THR ALA SEQRES 15 A 279 PRO GLU ALA ILE ALA TYR ARG LYS PHE THR SER ALA SER SEQRES 16 A 279 ASP VAL TRP SER TYR GLY ILE VAL MET TRP GLU VAL MET SEQRES 17 A 279 SER PHE GLY GLU ARG PRO TYR TRP ASP MET SER ASN GLN SEQRES 18 A 279 ASP VAL ILE ASN ALA ILE GLU GLN ASP TYR ARG LEU PRO SEQRES 19 A 279 PRO PRO MET ASP CYS PRO ALA ALA LEU HIS GLN LEU MET SEQRES 20 A 279 LEU ASP CYS TRP GLN LYS ASP ARG ASN SER ARG PRO ARG SEQRES 21 A 279 PHE ALA GLU ILE VAL ASN THR LEU ASP LYS MET ILE ARG SEQRES 22 A 279 ASN PRO ALA SER LEU LYS MODRES 7KPM PTR A 647 TYR MODIFIED RESIDUE HET PTR A 647 16 HET ADP A 901 27 HETNAM PTR O-PHOSPHOTYROSINE HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETSYN PTR PHOSPHONOTYROSINE FORMUL 1 PTR C9 H12 N O6 P FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 HOH *254(H2 O) HELIX 1 AA1 ASP A 615 SER A 617 5 3 HELIX 2 AA2 SER A 658 GLN A 674 1 17 HELIX 3 AA3 ALA A 704 GLN A 711 1 8 HELIX 4 AA4 THR A 717 MET A 738 1 22 HELIX 5 AA5 ALA A 746 ARG A 748 5 3 HELIX 6 AA6 PRO A 787 THR A 791 5 5 HELIX 7 AA7 ALA A 792 ARG A 799 1 8 HELIX 8 AA8 THR A 802 SER A 819 1 18 HELIX 9 AA9 SER A 829 GLN A 839 1 11 HELIX 10 AB1 PRO A 850 TRP A 861 1 12 HELIX 11 AB2 ASP A 864 ARG A 868 5 5 HELIX 12 AB3 ARG A 870 ASN A 884 1 15 HELIX 13 AB4 PRO A 885 LEU A 888 5 4 SHEET 1 AA1 5 VAL A 619 ALA A 627 0 SHEET 2 AA1 5 GLU A 632 LEU A 638 -1 O LYS A 635 N GLU A 623 SHEET 3 AA1 5 ILE A 646 THR A 652 -1 O ILE A 650 N TYR A 634 SHEET 4 AA1 5 MET A 694 GLU A 698 -1 O ILE A 695 N LYS A 651 SHEET 5 AA1 5 LEU A 683 VAL A 687 -1 N VAL A 687 O MET A 694 SHEET 1 AA2 2 ILE A 750 VAL A 752 0 SHEET 2 AA2 2 CYS A 758 VAL A 760 -1 O LYS A 759 N LEU A 751 LINK C ILE A 646 N PTR A 647 1555 1555 1.32 LINK C PTR A 647 N VAL A 648 1555 1555 1.35 CISPEP 1 ARG A 691 PRO A 692 0 -0.58 CRYST1 33.134 91.362 96.910 90.00 90.00 90.00 P 21 21 21 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 0.030180 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010945 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010319 0.00000