HEADER HYDROLASE 20-JUN-10 3NKM TITLE CRYSTAL STRUCTURE OF MOUSE AUTOTAXIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE FAMILY COMPND 3 MEMBER 2; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: ATX, E-NPP 2, AUTOTAXIN, EXTRACELLULAR LYSOPHOSPHOLIPASE D, COMPND 6 LYSOPLD; COMPND 7 EC: 3.1.4.39; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: ENPP2, NPPS2, PDNP2; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HEK293S GNT1-; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PCD-CW KEYWDS LYSOPHOSPHOLIPASE D, AUTOTAXIN, ENPP2, LYSOPHOSPHATIDIC ACID, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.NISHIMASU,R.ISHITANI,E.MIHARA,J.TAKAGI,J.AOKI,O.NUREKI REVDAT 4 29-JUL-20 3NKM 1 COMPND REMARK SEQADV HETNAM REVDAT 4 2 1 LINK SITE ATOM REVDAT 3 08-NOV-17 3NKM 1 REMARK REVDAT 2 19-FEB-14 3NKM 1 JRNL VERSN REVDAT 1 19-JAN-11 3NKM 0 JRNL AUTH H.NISHIMASU,S.OKUDAIRA,K.HAMA,E.MIHARA,N.DOHMAE,A.INOUE, JRNL AUTH 2 R.ISHITANI,J.TAKAGI,J.AOKI,O.NUREKI JRNL TITL CRYSTAL STRUCTURE OF AUTOTAXIN AND INSIGHT INTO GPCR JRNL TITL 2 ACTIVATION BY LIPID MEDIATORS JRNL REF NAT.STRUCT.MOL.BIOL. V. 18 205 2011 JRNL REFN ISSN 1545-9993 JRNL PMID 21240269 JRNL DOI 10.1038/NSMB.1998 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6_289 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.500 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 56804 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 2874 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 34.1877 - 5.5167 1.00 2701 134 0.1714 0.2081 REMARK 3 2 5.5167 - 4.3817 1.00 2649 151 0.1449 0.1704 REMARK 3 3 4.3817 - 3.8287 1.00 2612 169 0.1356 0.1836 REMARK 3 4 3.8287 - 3.4790 0.99 2620 148 0.1451 0.1829 REMARK 3 5 3.4790 - 3.2298 0.99 2616 139 0.1508 0.1907 REMARK 3 6 3.2298 - 3.0395 0.99 2610 140 0.1627 0.2452 REMARK 3 7 3.0395 - 2.8874 0.99 2607 146 0.1655 0.2016 REMARK 3 8 2.8874 - 2.7618 0.99 2607 138 0.1640 0.2312 REMARK 3 9 2.7618 - 2.6555 0.99 2609 118 0.1522 0.2137 REMARK 3 10 2.6555 - 2.5639 0.98 2580 135 0.1575 0.2235 REMARK 3 11 2.5639 - 2.4837 0.98 2617 132 0.1608 0.2106 REMARK 3 12 2.4837 - 2.4128 0.98 2571 125 0.1690 0.2169 REMARK 3 13 2.4128 - 2.3493 0.98 2556 150 0.1589 0.2493 REMARK 3 14 2.3493 - 2.2920 0.98 2575 143 0.1644 0.2303 REMARK 3 15 2.2920 - 2.2399 0.97 2569 156 0.1621 0.2395 REMARK 3 16 2.2399 - 2.1922 0.97 2522 128 0.1721 0.2278 REMARK 3 17 2.1922 - 2.1484 0.97 2581 135 0.1667 0.2385 REMARK 3 18 2.1484 - 2.1078 0.96 2528 119 0.1735 0.2455 REMARK 3 19 2.1078 - 2.0702 0.94 2508 137 0.1841 0.2281 REMARK 3 20 2.0702 - 2.0351 0.92 2414 112 0.1898 0.2664 REMARK 3 21 2.0351 - 2.0023 0.86 2278 119 0.2078 0.2638 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 : 0.35 REMARK 3 B_SOL : 40.22 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.560 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.56 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.48610 REMARK 3 B22 (A**2) : 3.80840 REMARK 3 B33 (A**2) : -5.29450 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.70400 REMARK 3 B23 (A**2) : 0.00000 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 : 0.007 6892 REMARK 3 ANGLE : 1.072 9320 REMARK 3 CHIRALITY : 0.071 1007 REMARK 3 PLANARITY : 0.005 1187 REMARK 3 DIHEDRAL : 19.504 2560 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 3NKM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000059947. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-FEB-10 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 : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NE3A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57920 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: SAD REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20-25% PEG 3350, 0.15MM NACL, 0.5M REMARK 280 KSCN, 0.2MM ZNSO4, 1% POLYVINYLPYRROLIDONE, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K 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 47.36550 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 ALA A 36 REMARK 465 GLU A 37 REMARK 465 TRP A 38 REMARK 465 ASP A 39 REMARK 465 GLU A 40 REMARK 465 GLY A 41 REMARK 465 PRO A 42 REMARK 465 PRO A 43 REMARK 465 THR A 44 REMARK 465 VAL A 45 REMARK 465 LEU A 46 REMARK 465 SER A 47 REMARK 465 ASP A 48 REMARK 465 SER A 49 REMARK 465 PRO A 50 REMARK 465 SER A 856 REMARK 465 GLU A 857 REMARK 465 ILE A 858 REMARK 465 SER A 859 REMARK 465 ARG A 860 REMARK 465 GLU A 861 REMARK 465 ASN A 862 REMARK 465 LEU A 863 REMARK 465 TYR A 864 REMARK 465 PHE A 865 REMARK 465 GLN A 866 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 A 59 CG CD CE NZ REMARK 470 GLU A 67 CG CD OE1 OE2 REMARK 470 LYS A 104 CG CD CE NZ REMARK 470 ARG A 162 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 244 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 246 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 274 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASN A 398 CG OD1 ND2 REMARK 470 LEU A 458 CG CD1 CD2 REMARK 470 LYS A 462 CG CD CE NZ REMARK 470 ARG A 549 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 559 CG CD OE1 NE2 REMARK 470 ARG A 602 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 642 CG CD OE1 OE2 REMARK 470 LYS A 666 CG CD CE NZ 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 CB CYS A 366 SG CYS A 468 1.56 REMARK 500 OG1 THR A 209 ZN ZN A 1001 1.63 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 ASN A 77 3.12 -66.50 REMARK 500 LEU A 94 49.70 -104.77 REMARK 500 ARG A 98 4.27 81.67 REMARK 500 GLU A 109 163.38 -46.66 REMARK 500 GLU A 113 4.33 -58.76 REMARK 500 ARG A 368 61.10 -111.94 REMARK 500 ALA A 435 -36.34 -156.17 REMARK 500 ARG A 450 -3.36 87.46 REMARK 500 ASP A 477 127.88 -31.89 REMARK 500 THR A 485 -163.97 -127.55 REMARK 500 ARG A 497 57.90 37.95 REMARK 500 SER A 672 -154.16 -112.52 REMARK 500 TRP A 810 -19.65 -152.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 NKP A 1007 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 NA A1004 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 2 O REMARK 620 2 ASN A 797 O 98.1 REMARK 620 3 SER A 800 O 90.0 77.1 REMARK 620 4 SER A 803 OG 164.0 88.9 77.5 REMARK 620 5 HOH A 980 O 84.2 177.1 101.0 88.5 REMARK 620 6 HOH A 986 O 97.1 82.1 158.8 98.1 99.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 171 OD1 REMARK 620 2 HIS A 359 NE2 105.0 REMARK 620 3 SO4 A1006 O2 109.7 114.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 311 OD1 REMARK 620 2 ASP A 311 OD2 52.7 REMARK 620 3 HIS A 315 NE2 103.1 88.7 REMARK 620 4 HIS A 474 NE2 96.8 148.4 108.9 REMARK 620 5 SO4 A1006 O3 133.2 98.2 113.0 98.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A1005 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 665 O REMARK 620 2 ASP A 668 O 67.1 REMARK 620 3 MET A 671 O 82.5 66.2 REMARK 620 4 HOH A1144 O 82.7 143.5 90.8 REMARK 620 5 HOH A1147 O 79.8 86.0 151.2 109.1 REMARK 620 6 HOH A1343 O 165.9 98.8 91.3 110.1 100.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1003 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 735 OD1 REMARK 620 2 ASN A 737 OD1 81.1 REMARK 620 3 ASN A 739 OD1 80.0 84.0 REMARK 620 4 LEU A 741 O 91.7 166.4 83.3 REMARK 620 5 ASP A 743 OD1 100.0 86.5 170.4 106.2 REMARK 620 6 HOH A 880 O 169.0 92.8 90.3 92.2 88.8 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3NKN RELATED DB: PDB REMARK 900 RELATED ID: 3NKO RELATED DB: PDB REMARK 900 RELATED ID: 3NKP RELATED DB: PDB REMARK 900 RELATED ID: 3NKQ RELATED DB: PDB REMARK 900 RELATED ID: 3NKR RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 PROTEIN USED IN THIS STRUCTURE IS AN ISOFORM OF ANTOTAXIN FROM REMARK 999 MOUSE, WHICH IS LACK OF RESIDUES KVEP (UNP RESDIUES 571-574 OF REMARK 999 DATABASE ENPP2_MOUSE). DBREF 3NKM A 36 858 UNP Q9R1E6 ENPP2_MOUSE 36 862 SEQADV 3NKM A UNP Q9R1E6 LYS 571 SEE REMARK 999 SEQADV 3NKM A UNP Q9R1E6 VAL 572 SEE REMARK 999 SEQADV 3NKM A UNP Q9R1E6 GLU 573 SEE REMARK 999 SEQADV 3NKM A UNP Q9R1E6 PRO 574 SEE REMARK 999 SEQADV 3NKM SER A 859 UNP Q9R1E6 EXPRESSION TAG SEQADV 3NKM ARG A 860 UNP Q9R1E6 EXPRESSION TAG SEQADV 3NKM GLU A 861 UNP Q9R1E6 EXPRESSION TAG SEQADV 3NKM ASN A 862 UNP Q9R1E6 EXPRESSION TAG SEQADV 3NKM LEU A 863 UNP Q9R1E6 EXPRESSION TAG SEQADV 3NKM TYR A 864 UNP Q9R1E6 EXPRESSION TAG SEQADV 3NKM PHE A 865 UNP Q9R1E6 EXPRESSION TAG SEQADV 3NKM GLN A 866 UNP Q9R1E6 EXPRESSION TAG SEQRES 1 A 831 ALA GLU TRP ASP GLU GLY PRO PRO THR VAL LEU SER ASP SEQRES 2 A 831 SER PRO TRP THR ASN THR SER GLY SER CYS LYS GLY ARG SEQRES 3 A 831 CYS PHE GLU LEU GLN GLU VAL GLY PRO PRO ASP CYS ARG SEQRES 4 A 831 CYS ASP ASN LEU CYS LYS SER TYR SER SER CYS CYS HIS SEQRES 5 A 831 ASP PHE ASP GLU LEU CYS LEU LYS THR ALA ARG GLY TRP SEQRES 6 A 831 GLU CYS THR LYS ASP ARG CYS GLY GLU VAL ARG ASN GLU SEQRES 7 A 831 GLU ASN ALA CYS HIS CYS SER GLU ASP CYS LEU SER ARG SEQRES 8 A 831 GLY ASP CYS CYS THR ASN TYR GLN VAL VAL CYS LYS GLY SEQRES 9 A 831 GLU SER HIS TRP VAL ASP ASP ASP CYS GLU GLU ILE ARG SEQRES 10 A 831 VAL PRO GLU CYS PRO ALA GLY PHE VAL ARG PRO PRO LEU SEQRES 11 A 831 ILE ILE PHE SER VAL ASP GLY PHE ARG ALA SER TYR MET SEQRES 12 A 831 LYS LYS GLY SER LYS VAL MET PRO ASN ILE GLU LYS LEU SEQRES 13 A 831 ARG SER CYS GLY THR HIS ALA PRO TYR MET ARG PRO VAL SEQRES 14 A 831 TYR PRO THR LYS THR PHE PRO ASN LEU TYR THR LEU ALA SEQRES 15 A 831 THR GLY LEU TYR PRO GLU SER HIS GLY ILE VAL GLY ASN SEQRES 16 A 831 SER MET TYR ASP PRO VAL PHE ASP ALA THR PHE HIS LEU SEQRES 17 A 831 ARG GLY ARG GLU LYS PHE ASN HIS ARG TRP TRP GLY GLY SEQRES 18 A 831 GLN PRO LEU TRP ILE THR ALA THR LYS GLN GLY VAL ARG SEQRES 19 A 831 ALA GLY THR PHE PHE TRP SER VAL SER ILE PRO HIS GLU SEQRES 20 A 831 ARG ARG ILE LEU THR ILE LEU GLN TRP LEU SER LEU PRO SEQRES 21 A 831 ASP ASN GLU ARG PRO SER VAL TYR ALA PHE TYR SER GLU SEQRES 22 A 831 GLN PRO ASP PHE SER GLY HIS LYS TYR GLY PRO PHE GLY SEQRES 23 A 831 PRO GLU MET THR ASN PRO LEU ARG GLU ILE ASP LYS THR SEQRES 24 A 831 VAL GLY GLN LEU MET ASP GLY LEU LYS GLN LEU LYS LEU SEQRES 25 A 831 HIS ARG CYS VAL ASN VAL ILE PHE VAL GLY ASP HIS GLY SEQRES 26 A 831 MET GLU ASP VAL THR CYS ASP ARG THR GLU PHE LEU SER SEQRES 27 A 831 ASN TYR LEU THR ASN VAL ASP ASP ILE THR LEU VAL PRO SEQRES 28 A 831 GLY THR LEU GLY ARG ILE ARG PRO LYS ILE PRO ASN ASN SEQRES 29 A 831 LEU LYS TYR ASP PRO LYS ALA ILE ILE ALA ASN LEU THR SEQRES 30 A 831 CYS LYS LYS PRO ASP GLN HIS PHE LYS PRO TYR MET LYS SEQRES 31 A 831 GLN HIS LEU PRO LYS ARG LEU HIS TYR ALA ASN ASN ARG SEQRES 32 A 831 ARG ILE GLU ASP LEU HIS LEU LEU VAL GLU ARG ARG TRP SEQRES 33 A 831 HIS VAL ALA ARG LYS PRO LEU ASP VAL TYR LYS LYS PRO SEQRES 34 A 831 SER GLY LYS CYS PHE PHE GLN GLY ASP HIS GLY PHE ASP SEQRES 35 A 831 ASN LYS VAL ASN SER MET GLN THR VAL PHE VAL GLY TYR SEQRES 36 A 831 GLY PRO THR PHE LYS TYR ARG THR LYS VAL PRO PRO PHE SEQRES 37 A 831 GLU ASN ILE GLU LEU TYR ASN VAL MET CYS ASP LEU LEU SEQRES 38 A 831 GLY LEU LYS PRO ALA PRO ASN ASN GLY THR HIS GLY SER SEQRES 39 A 831 LEU ASN HIS LEU LEU ARG THR ASN THR PHE ARG PRO THR SEQRES 40 A 831 LEU PRO GLU GLU VAL SER ARG PRO ASN TYR PRO GLY ILE SEQRES 41 A 831 MET TYR LEU GLN SER ASP PHE ASP LEU GLY CYS THR CYS SEQRES 42 A 831 ASP ASP LYS ASN LYS LEU GLU GLU LEU ASN LYS ARG LEU SEQRES 43 A 831 HIS THR LYS GLY SER THR GLU GLU ARG HIS LEU LEU TYR SEQRES 44 A 831 GLY ARG PRO ALA VAL LEU TYR ARG THR SER TYR ASP ILE SEQRES 45 A 831 LEU TYR HIS THR ASP PHE GLU SER GLY TYR SER GLU ILE SEQRES 46 A 831 PHE LEU MET PRO LEU TRP THR SER TYR THR ILE SER LYS SEQRES 47 A 831 GLN ALA GLU VAL SER SER ILE PRO GLU HIS LEU THR ASN SEQRES 48 A 831 CYS VAL ARG PRO ASP VAL ARG VAL SER PRO GLY PHE SER SEQRES 49 A 831 GLN ASN CYS LEU ALA TYR LYS ASN ASP LYS GLN MET SER SEQRES 50 A 831 TYR GLY PHE LEU PHE PRO PRO TYR LEU SER SER SER PRO SEQRES 51 A 831 GLU ALA LYS TYR ASP ALA PHE LEU VAL THR ASN MET VAL SEQRES 52 A 831 PRO MET TYR PRO ALA PHE LYS ARG VAL TRP THR TYR PHE SEQRES 53 A 831 GLN ARG VAL LEU VAL LYS LYS TYR ALA SER GLU ARG ASN SEQRES 54 A 831 GLY VAL ASN VAL ILE SER GLY PRO ILE PHE ASP TYR ASN SEQRES 55 A 831 TYR ASN GLY LEU ARG ASP ILE GLU ASP GLU ILE LYS GLN SEQRES 56 A 831 TYR VAL GLU GLY SER SER ILE PRO VAL PRO THR HIS TYR SEQRES 57 A 831 TYR SER ILE ILE THR SER CYS LEU ASP PHE THR GLN PRO SEQRES 58 A 831 ALA ASP LYS CYS ASP GLY PRO LEU SER VAL SER SER PHE SEQRES 59 A 831 ILE LEU PRO HIS ARG PRO ASP ASN ASP GLU SER CYS ASN SEQRES 60 A 831 SER SER GLU ASP GLU SER LYS TRP VAL GLU GLU LEU MET SEQRES 61 A 831 LYS MET HIS THR ALA ARG VAL ARG ASP ILE GLU HIS LEU SEQRES 62 A 831 THR GLY LEU ASP PHE TYR ARG LYS THR SER ARG SER TYR SEQRES 63 A 831 SER GLU ILE LEU THR LEU LYS THR TYR LEU HIS THR TYR SEQRES 64 A 831 GLU SER GLU ILE SER ARG GLU ASN LEU TYR PHE GLN MODRES 3NKM ASN A 524 ASN GLYCOSYLATION SITE MODRES 3NKM ASN A 410 ASN GLYCOSYLATION SITE MODRES 3NKM ASN A 53 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET NAG C 1 14 HET NAG C 2 14 HET BMA C 3 11 HET MAN C 4 11 HET MAN C 5 11 HET MAN C 6 11 HET NAG D 1 14 HET NAG D 2 14 HET ZN A1001 1 HET ZN A1002 1 HET CA A1003 1 HET NA A1004 1 HET K A1005 1 HET SO4 A1006 5 HET NKP A1007 6 HET SCN A1008 3 HET SCN A1009 3 HET EDO A1010 4 HET EDO A1011 4 HET EDO A1012 4 HET EDO A1013 4 HET EDO A1014 4 HET EDO A1015 4 HET EDO A1016 4 HET EDO A1017 4 HET EDO A1018 4 HET EDO A1019 4 HET EDO A1020 4 HET EDO A1021 4 HET EDO A1022 4 HET EDO A1023 4 HET EDO A1024 4 HET EDO A1025 4 HET EDO A1026 4 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM NA SODIUM ION HETNAM K POTASSIUM ION HETNAM SO4 SULFATE ION HETNAM NKP (2R)-2-HYDROXY-3-(PHOSPHONOOXY)PROPYL (9E)-OCTADEC-9- HETNAM 2 NKP ENOATE HETNAM SCN THIOCYANATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN NKP 18:1 LPA, OLEOYL LYSOPHOSPHATIDIC ACID HETSYN EDO ETHYLENE GLYCOL FORMUL 2 NAG 6(C8 H15 N O6) FORMUL 3 BMA C6 H12 O6 FORMUL 3 MAN 3(C6 H12 O6) FORMUL 5 ZN 2(ZN 2+) FORMUL 7 CA CA 2+ FORMUL 8 NA NA 1+ FORMUL 9 K K 1+ FORMUL 10 SO4 O4 S 2- FORMUL 11 NKP C21 H41 O7 P FORMUL 12 SCN 2(C N S 1-) FORMUL 14 EDO 17(C2 H6 O2) FORMUL 31 HOH *712(H2 O) HELIX 1 1 CYS A 79 SER A 83 5 5 HELIX 2 2 ASP A 88 LEU A 94 1 7 HELIX 3 3 THR A 103 CYS A 107 5 5 HELIX 4 4 ASP A 122 GLY A 127 1 6 HELIX 5 5 ASN A 132 LYS A 138 1 7 HELIX 6 6 HIS A 142 ASP A 146 5 5 HELIX 7 7 ARG A 174 LYS A 179 5 6 HELIX 8 8 LYS A 180 MET A 185 1 6 HELIX 9 9 MET A 185 GLY A 195 1 11 HELIX 10 10 LYS A 208 GLY A 219 1 12 HELIX 11 11 TYR A 221 GLY A 226 1 6 HELIX 12 12 ARG A 246 TRP A 254 5 9 HELIX 13 13 PRO A 258 GLN A 266 1 9 HELIX 14 14 PRO A 280 SER A 293 1 14 HELIX 15 15 ASP A 311 GLY A 318 1 8 HELIX 16 16 GLY A 321 GLU A 323 5 3 HELIX 17 17 MET A 324 LEU A 345 1 22 HELIX 18 18 SER A 373 TYR A 375 5 3 HELIX 19 19 ASN A 378 ASP A 380 5 3 HELIX 20 20 ASP A 403 THR A 412 1 10 HELIX 21 21 GLN A 426 LEU A 428 5 3 HELIX 22 22 PRO A 429 HIS A 433 5 5 HELIX 23 23 LYS A 456 VAL A 460 5 5 HELIX 24 24 VAL A 480 GLN A 484 5 5 HELIX 25 25 GLU A 507 LEU A 516 1 10 HELIX 26 26 LEU A 530 LEU A 534 5 5 HELIX 27 27 LEU A 558 PHE A 562 5 5 HELIX 28 28 LEU A 574 ASN A 578 5 5 HELIX 29 29 SER A 586 LEU A 592 1 7 HELIX 30 30 PRO A 641 THR A 645 5 5 HELIX 31 31 SER A 655 SER A 659 5 5 HELIX 32 32 ASN A 661 ASP A 668 1 8 HELIX 33 33 PRO A 678 SER A 682 5 5 HELIX 34 34 GLU A 686 THR A 695 5 10 HELIX 35 35 TYR A 701 VAL A 714 1 14 HELIX 36 36 VAL A 714 ASN A 724 1 11 HELIX 37 37 ILE A 744 ILE A 748 5 5 HELIX 38 38 PRO A 776 CYS A 780 5 5 HELIX 39 39 ASP A 806 LYS A 809 5 4 HELIX 40 40 TRP A 810 HIS A 818 1 9 HELIX 41 41 ARG A 821 GLY A 830 1 10 HELIX 42 42 SER A 840 TYR A 850 1 11 SHEET 1 A 6 VAL A 302 PRO A 310 0 SHEET 2 A 6 LEU A 165 ASP A 171 1 N ILE A 167 O PHE A 305 SHEET 3 A 6 ASN A 352 GLY A 357 1 O ILE A 354 N PHE A 168 SHEET 4 A 6 PHE A 487 TYR A 490 -1 O TYR A 490 N VAL A 353 SHEET 5 A 6 THR A 196 HIS A 197 -1 N THR A 196 O GLY A 489 SHEET 6 A 6 THR A 498 LYS A 499 1 O THR A 498 N HIS A 197 SHEET 1 B 2 MET A 201 ARG A 202 0 SHEET 2 B 2 PHE A 503 GLU A 504 1 O PHE A 503 N ARG A 202 SHEET 1 C 2 MET A 232 ASP A 234 0 SHEET 2 C 2 ALA A 239 PHE A 241 -1 O PHE A 241 N MET A 232 SHEET 1 D 2 GLU A 362 ASP A 363 0 SHEET 2 D 2 GLY A 472 ASP A 473 -1 O ASP A 473 N GLU A 362 SHEET 1 E 2 THR A 369 PHE A 371 0 SHEET 2 E 2 HIS A 452 ALA A 454 1 O HIS A 452 N GLU A 370 SHEET 1 F 4 ILE A 382 VAL A 385 0 SHEET 2 F 4 LEU A 389 PRO A 394 -1 O ARG A 393 N THR A 383 SHEET 3 F 4 LEU A 443 VAL A 447 -1 O LEU A 445 N GLY A 390 SHEET 4 F 4 PHE A 420 MET A 424 -1 N TYR A 423 O HIS A 444 SHEET 1 G 2 ALA A 598 VAL A 599 0 SHEET 2 G 2 LEU A 831 ASP A 832 -1 O ASP A 832 N ALA A 598 SHEET 1 H 7 TYR A 605 TYR A 609 0 SHEET 2 H 7 GLU A 614 SER A 618 -1 O TYR A 617 N ASP A 606 SHEET 3 H 7 PRO A 624 ILE A 631 -1 O SER A 628 N GLU A 614 SHEET 4 H 7 VAL A 726 ILE A 733 -1 O VAL A 728 N TYR A 629 SHEET 5 H 7 HIS A 762 CYS A 770 -1 O THR A 768 N ASN A 727 SHEET 6 H 7 LEU A 784 PRO A 792 -1 O SER A 787 N ILE A 767 SHEET 7 H 7 THR A 819 ALA A 820 -1 O ALA A 820 N SER A 788 SHEET 1 I 2 SER A 672 PHE A 675 0 SHEET 2 I 2 MET A 697 MET A 700 -1 O VAL A 698 N GLY A 674 SSBOND 1 CYS A 58 CYS A 75 1555 1555 2.03 SSBOND 2 CYS A 62 CYS A 93 1555 1555 2.04 SSBOND 3 CYS A 73 CYS A 86 1555 1555 2.04 SSBOND 4 CYS A 79 CYS A 85 1555 1555 2.02 SSBOND 5 CYS A 102 CYS A 119 1555 1555 2.04 SSBOND 6 CYS A 107 CYS A 137 1555 1555 2.04 SSBOND 7 CYS A 117 CYS A 130 1555 1555 2.03 SSBOND 8 CYS A 123 CYS A 129 1555 1555 2.03 SSBOND 9 CYS A 148 CYS A 194 1555 1555 2.02 SSBOND 10 CYS A 156 CYS A 350 1555 1555 2.02 SSBOND 11 CYS A 366 CYS A 468 1555 1555 2.02 SSBOND 12 CYS A 413 CYS A 801 1555 1555 2.03 SSBOND 13 CYS A 566 CYS A 662 1555 1555 2.04 SSBOND 14 CYS A 568 CYS A 647 1555 1555 2.04 SSBOND 15 CYS A 770 CYS A 780 1555 1555 2.04 LINK ND2 ASN A 53 C1 NAG B 1 1555 1555 1.44 LINK ND2 ASN A 410 C1 NAG D 1 1555 1555 1.44 LINK ND2 ASN A 524 C1 NAG C 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 1.44 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.44 LINK O6 BMA C 3 C1 MAN C 4 1555 1555 1.45 LINK O3 MAN C 4 C1 MAN C 5 1555 1555 1.45 LINK O2 MAN C 5 C1 MAN C 6 1555 1555 1.44 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.44 LINK O HOH A 2 NA NA A1004 1555 1555 2.59 LINK OD1 ASP A 171 ZN ZN A1001 1555 1555 1.90 LINK OD1 ASP A 311 ZN ZN A1002 1555 1555 2.14 LINK OD2 ASP A 311 ZN ZN A1002 1555 1555 2.65 LINK NE2 HIS A 315 ZN ZN A1002 1555 1555 1.96 LINK NE2 HIS A 359 ZN ZN A1001 1555 1555 2.19 LINK NE2 HIS A 474 ZN ZN A1002 1555 1555 2.07 LINK O TYR A 665 K K A1005 1555 1555 3.12 LINK O ASP A 668 K K A1005 1555 1555 3.07 LINK O MET A 671 K K A1005 1555 1555 3.01 LINK OD1 ASP A 735 CA CA A1003 1555 1555 2.45 LINK OD1 ASN A 737 CA CA A1003 1555 1555 2.46 LINK OD1 ASN A 739 CA CA A1003 1555 1555 2.52 LINK O LEU A 741 CA CA A1003 1555 1555 2.40 LINK OD1 ASP A 743 CA CA A1003 1555 1555 2.39 LINK O ASN A 797 NA NA A1004 1555 1555 2.59 LINK O SER A 800 NA NA A1004 1555 1555 2.71 LINK OG SER A 803 NA NA A1004 1555 1555 2.61 LINK O HOH A 880 CA CA A1003 1555 1555 2.53 LINK O HOH A 980 NA NA A1004 1555 1555 2.65 LINK O HOH A 986 NA NA A1004 1555 1555 2.71 LINK ZN ZN A1001 O2 SO4 A1006 1555 1555 2.19 LINK ZN ZN A1002 O3 SO4 A1006 1555 1555 2.08 LINK K K A1005 O HOH A1144 1555 1555 3.31 LINK K K A1005 O HOH A1147 1555 1555 3.45 LINK K K A1005 O HOH A1343 1555 1555 3.44 CISPEP 1 PRO A 70 PRO A 71 0 1.67 CISPEP 2 TYR A 205 PRO A 206 0 -3.21 CISPEP 3 GLN A 309 PRO A 310 0 6.98 CRYST1 61.588 94.731 75.652 90.00 94.05 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 0.016237 0.000000 0.001150 0.00000 SCALE2 0.000000 0.010556 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013252 0.00000