HEADER SIGNALING PROTEIN 03-APR-19 6R9H TITLE CRYSTAL STRUCTURE OF THE PDZ TANDEM OF SYNTENIN IN COMPLEX WITH TITLE 2 FRAGMENT C58 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNTENIN-1; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: MELANOMA DIFFERENTIATION-ASSOCIATED PROTEIN 9,MDA-9,PRO-TGF- COMPND 5 ALPHA CYTOPLASMIC DOMAIN-INTERACTING PROTEIN 18,TACIP18,SCAFFOLD COMPND 6 PROTEIN PBP1,SYNDECAN-BINDING PROTEIN 1; COMPND 7 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: SDCBP, MDA9, SYCL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 83333 KEYWDS SIGNALING PROTEIN CELL ADHESION PDZ DOMAIN SYNTENIN SYNDECAN DRUG KEYWDS 2 DESIGN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.FERACCI,K.BARRAL REVDAT 2 24-JAN-24 6R9H 1 JRNL REVDAT 1 03-FEB-21 6R9H 0 JRNL AUTH R.LEBLANC,R.KASHYAP,K.BARRAL,A.L.EGEA-JIMENEZ,D.KOVALSKYY, JRNL AUTH 2 M.FERACCI,M.GARCIA,C.DERVIAUX,S.BETZI,R.GHOSSOUB,M.PLATONOV, JRNL AUTH 3 P.ROCHE,X.MORELLI,L.HOFFER,P.ZIMMERMANN JRNL TITL PHARMACOLOGICAL INHIBITION OF SYNTENIN PDZ2 DOMAIN IMPAIRS JRNL TITL 2 BREAST CANCER CELL ACTIVITIES AND EXOSOME LOADIFING WITH JRNL TITL 3 SYNDECAN AND EPCAM CARGO. JRNL REF J EXTRACELL VESICLES V. 10 12039 2020 JRNL REFN ESSN 2001-3078 JRNL PMID 33343836 JRNL DOI 10.1002/JEV2.12039 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 36490 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4061 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2716 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.66 REMARK 3 BIN R VALUE (WORKING SET) : 0.3090 REMARK 3 BIN FREE R VALUE SET COUNT : 298 REMARK 3 BIN FREE R VALUE : 0.3220 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4958 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 70 REMARK 3 SOLVENT ATOMS : 262 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.18 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.75000 REMARK 3 B22 (A**2) : -0.65000 REMARK 3 B33 (A**2) : -2.11000 REMARK 3 B12 (A**2) : -0.58000 REMARK 3 B13 (A**2) : -0.10000 REMARK 3 B23 (A**2) : 0.47000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.256 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.196 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.156 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.858 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5101 ; 0.008 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 4878 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6873 ; 1.515 ; 1.639 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11339 ; 1.246 ; 1.592 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 651 ; 7.110 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 240 ;35.277 ;23.417 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 943 ;15.490 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;25.477 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 711 ; 0.063 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5657 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 971 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2613 ; 2.358 ; 3.127 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2609 ; 2.354 ; 3.127 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3261 ; 3.535 ; 4.680 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3260 ; 3.534 ; 4.680 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2488 ; 3.336 ; 3.647 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2489 ; 3.335 ; 3.647 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3613 ; 5.094 ; 5.282 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5430 ; 7.012 ;37.818 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5431 ; 7.012 ;37.818 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 6 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 111 272 B 111 272 4582 0.11 0.05 REMARK 3 2 A 111 271 C 111 271 4593 0.10 0.05 REMARK 3 3 A 111 271 D 111 271 4589 0.11 0.05 REMARK 3 4 B 111 271 C 111 271 4561 0.11 0.05 REMARK 3 5 B 111 271 D 111 271 4582 0.11 0.05 REMARK 3 6 C 111 272 D 111 272 4641 0.11 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6R9H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-APR-19. REMARK 100 THE DEPOSITION ID IS D_1292101600. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-NOV-17 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 : ESRF REMARK 200 BEAMLINE : ID30B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40550 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 45.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.08739 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.5700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.68900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.530 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: 1W9E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM ACETATE PH 4.6, 200MM REMARK 280 AMMONIUM ACETATE, 22% PEG 3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 GLY A 108 REMARK 465 ALA A 109 REMARK 465 MET A 110 REMARK 465 PHE A 273 REMARK 465 GLY B 108 REMARK 465 ALA B 109 REMARK 465 MET B 110 REMARK 465 PHE B 273 REMARK 465 GLY C 108 REMARK 465 ALA C 109 REMARK 465 GLY D 108 REMARK 465 ALA D 109 REMARK 465 MET D 110 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 PHE A 154 125.50 -38.82 REMARK 500 ARG A 193 73.07 14.60 REMARK 500 PHE B 154 123.63 -35.87 REMARK 500 ARG B 193 70.52 17.01 REMARK 500 PHE C 154 125.57 -39.79 REMARK 500 ARG C 193 69.69 15.72 REMARK 500 ARG C 193 69.69 16.50 REMARK 500 PHE D 154 123.52 -37.08 REMARK 500 ARG D 193 72.31 15.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue JVK A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue JVK C 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 D 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT D 302 DBREF 6R9H A 113 273 UNP O00560 SDCB1_HUMAN 113 273 DBREF 6R9H B 113 273 UNP O00560 SDCB1_HUMAN 113 273 DBREF 6R9H C 113 273 UNP O00560 SDCB1_HUMAN 113 273 DBREF 6R9H D 113 273 UNP O00560 SDCB1_HUMAN 113 273 SEQADV 6R9H GLY A 108 UNP O00560 EXPRESSION TAG SEQADV 6R9H ALA A 109 UNP O00560 EXPRESSION TAG SEQADV 6R9H MET A 110 UNP O00560 EXPRESSION TAG SEQADV 6R9H ASP A 111 UNP O00560 EXPRESSION TAG SEQADV 6R9H PRO A 112 UNP O00560 EXPRESSION TAG SEQADV 6R9H GLY B 108 UNP O00560 EXPRESSION TAG SEQADV 6R9H ALA B 109 UNP O00560 EXPRESSION TAG SEQADV 6R9H MET B 110 UNP O00560 EXPRESSION TAG SEQADV 6R9H ASP B 111 UNP O00560 EXPRESSION TAG SEQADV 6R9H PRO B 112 UNP O00560 EXPRESSION TAG SEQADV 6R9H GLY C 108 UNP O00560 EXPRESSION TAG SEQADV 6R9H ALA C 109 UNP O00560 EXPRESSION TAG SEQADV 6R9H MET C 110 UNP O00560 EXPRESSION TAG SEQADV 6R9H ASP C 111 UNP O00560 EXPRESSION TAG SEQADV 6R9H PRO C 112 UNP O00560 EXPRESSION TAG SEQADV 6R9H GLY D 108 UNP O00560 EXPRESSION TAG SEQADV 6R9H ALA D 109 UNP O00560 EXPRESSION TAG SEQADV 6R9H MET D 110 UNP O00560 EXPRESSION TAG SEQADV 6R9H ASP D 111 UNP O00560 EXPRESSION TAG SEQADV 6R9H PRO D 112 UNP O00560 EXPRESSION TAG SEQRES 1 A 166 GLY ALA MET ASP PRO ARG GLU VAL ILE LEU CYS LYS ASP SEQRES 2 A 166 GLN ASP GLY LYS ILE GLY LEU ARG LEU LYS SER ILE ASP SEQRES 3 A 166 ASN GLY ILE PHE VAL GLN LEU VAL GLN ALA ASN SER PRO SEQRES 4 A 166 ALA SER LEU VAL GLY LEU ARG PHE GLY ASP GLN VAL LEU SEQRES 5 A 166 GLN ILE ASN GLY GLU ASN CYS ALA GLY TRP SER SER ASP SEQRES 6 A 166 LYS ALA HIS LYS VAL LEU LYS GLN ALA PHE GLY GLU LYS SEQRES 7 A 166 ILE THR MET THR ILE ARG ASP ARG PRO PHE GLU ARG THR SEQRES 8 A 166 ILE THR MET HIS LYS ASP SER THR GLY HIS VAL GLY PHE SEQRES 9 A 166 ILE PHE LYS ASN GLY LYS ILE THR SER ILE VAL LYS ASP SEQRES 10 A 166 SER SER ALA ALA ARG ASN GLY LEU LEU THR GLU HIS ASN SEQRES 11 A 166 ILE CYS GLU ILE ASN GLY GLN ASN VAL ILE GLY LEU LYS SEQRES 12 A 166 ASP SER GLN ILE ALA ASP ILE LEU SER THR SER GLY THR SEQRES 13 A 166 VAL VAL THR ILE THR ILE MET PRO ALA PHE SEQRES 1 B 166 GLY ALA MET ASP PRO ARG GLU VAL ILE LEU CYS LYS ASP SEQRES 2 B 166 GLN ASP GLY LYS ILE GLY LEU ARG LEU LYS SER ILE ASP SEQRES 3 B 166 ASN GLY ILE PHE VAL GLN LEU VAL GLN ALA ASN SER PRO SEQRES 4 B 166 ALA SER LEU VAL GLY LEU ARG PHE GLY ASP GLN VAL LEU SEQRES 5 B 166 GLN ILE ASN GLY GLU ASN CYS ALA GLY TRP SER SER ASP SEQRES 6 B 166 LYS ALA HIS LYS VAL LEU LYS GLN ALA PHE GLY GLU LYS SEQRES 7 B 166 ILE THR MET THR ILE ARG ASP ARG PRO PHE GLU ARG THR SEQRES 8 B 166 ILE THR MET HIS LYS ASP SER THR GLY HIS VAL GLY PHE SEQRES 9 B 166 ILE PHE LYS ASN GLY LYS ILE THR SER ILE VAL LYS ASP SEQRES 10 B 166 SER SER ALA ALA ARG ASN GLY LEU LEU THR GLU HIS ASN SEQRES 11 B 166 ILE CYS GLU ILE ASN GLY GLN ASN VAL ILE GLY LEU LYS SEQRES 12 B 166 ASP SER GLN ILE ALA ASP ILE LEU SER THR SER GLY THR SEQRES 13 B 166 VAL VAL THR ILE THR ILE MET PRO ALA PHE SEQRES 1 C 166 GLY ALA MET ASP PRO ARG GLU VAL ILE LEU CYS LYS ASP SEQRES 2 C 166 GLN ASP GLY LYS ILE GLY LEU ARG LEU LYS SER ILE ASP SEQRES 3 C 166 ASN GLY ILE PHE VAL GLN LEU VAL GLN ALA ASN SER PRO SEQRES 4 C 166 ALA SER LEU VAL GLY LEU ARG PHE GLY ASP GLN VAL LEU SEQRES 5 C 166 GLN ILE ASN GLY GLU ASN CYS ALA GLY TRP SER SER ASP SEQRES 6 C 166 LYS ALA HIS LYS VAL LEU LYS GLN ALA PHE GLY GLU LYS SEQRES 7 C 166 ILE THR MET THR ILE ARG ASP ARG PRO PHE GLU ARG THR SEQRES 8 C 166 ILE THR MET HIS LYS ASP SER THR GLY HIS VAL GLY PHE SEQRES 9 C 166 ILE PHE LYS ASN GLY LYS ILE THR SER ILE VAL LYS ASP SEQRES 10 C 166 SER SER ALA ALA ARG ASN GLY LEU LEU THR GLU HIS ASN SEQRES 11 C 166 ILE CYS GLU ILE ASN GLY GLN ASN VAL ILE GLY LEU LYS SEQRES 12 C 166 ASP SER GLN ILE ALA ASP ILE LEU SER THR SER GLY THR SEQRES 13 C 166 VAL VAL THR ILE THR ILE MET PRO ALA PHE SEQRES 1 D 166 GLY ALA MET ASP PRO ARG GLU VAL ILE LEU CYS LYS ASP SEQRES 2 D 166 GLN ASP GLY LYS ILE GLY LEU ARG LEU LYS SER ILE ASP SEQRES 3 D 166 ASN GLY ILE PHE VAL GLN LEU VAL GLN ALA ASN SER PRO SEQRES 4 D 166 ALA SER LEU VAL GLY LEU ARG PHE GLY ASP GLN VAL LEU SEQRES 5 D 166 GLN ILE ASN GLY GLU ASN CYS ALA GLY TRP SER SER ASP SEQRES 6 D 166 LYS ALA HIS LYS VAL LEU LYS GLN ALA PHE GLY GLU LYS SEQRES 7 D 166 ILE THR MET THR ILE ARG ASP ARG PRO PHE GLU ARG THR SEQRES 8 D 166 ILE THR MET HIS LYS ASP SER THR GLY HIS VAL GLY PHE SEQRES 9 D 166 ILE PHE LYS ASN GLY LYS ILE THR SER ILE VAL LYS ASP SEQRES 10 D 166 SER SER ALA ALA ARG ASN GLY LEU LEU THR GLU HIS ASN SEQRES 11 D 166 ILE CYS GLU ILE ASN GLY GLN ASN VAL ILE GLY LEU LYS SEQRES 12 D 166 ASP SER GLN ILE ALA ASP ILE LEU SER THR SER GLY THR SEQRES 13 D 166 VAL VAL THR ILE THR ILE MET PRO ALA PHE HET PO4 A 301 5 HET PO4 A 302 5 HET JVK A 303 19 HET ACT A 304 4 HET ACT B 301 4 HET PO4 C 301 5 HET JVK C 302 19 HET PO4 D 301 5 HET ACT D 302 4 HETNAM PO4 PHOSPHATE ION HETNAM JVK (2~{S})-2-[2-(4-CHLOROPHENYL)SULFANYLETHANOYLAMINO]-3- HETNAM 2 JVK METHYL-BUTANOIC ACID HETNAM ACT ACETATE ION FORMUL 5 PO4 4(O4 P 3-) FORMUL 7 JVK 2(C13 H16 CL N O3 S) FORMUL 8 ACT 3(C2 H3 O2 1-) FORMUL 14 HOH *262(H2 O) HELIX 1 AA1 SER A 145 VAL A 150 1 6 HELIX 2 AA2 SER A 170 ALA A 181 1 12 HELIX 3 AA3 SER A 225 ASN A 230 1 6 HELIX 4 AA4 LYS A 250 SER A 261 1 12 HELIX 5 AA5 SER B 145 VAL B 150 1 6 HELIX 6 AA6 SER B 170 ALA B 181 1 12 HELIX 7 AA7 SER B 225 GLY B 231 1 7 HELIX 8 AA8 LYS B 250 SER B 261 1 12 HELIX 9 AA9 SER C 145 VAL C 150 1 6 HELIX 10 AB1 SER C 170 ALA C 181 1 12 HELIX 11 AB2 SER C 225 ASN C 230 1 6 HELIX 12 AB3 LYS C 250 SER C 261 1 12 HELIX 13 AB4 SER D 145 VAL D 150 1 6 HELIX 14 AB5 SER D 170 ALA D 181 1 12 HELIX 15 AB6 SER D 225 ASN D 230 1 6 HELIX 16 AB7 LYS D 250 SER D 261 1 12 SHEET 1 AA1 5 ARG A 113 CYS A 118 0 SHEET 2 AA1 5 LYS A 185 ARG A 191 -1 O ILE A 190 N ARG A 113 SHEET 3 AA1 5 GLN A 157 ILE A 161 -1 N GLN A 157 O ARG A 191 SHEET 4 AA1 5 GLY A 135 VAL A 141 -1 N ILE A 136 O VAL A 158 SHEET 5 AA1 5 LEU A 127 ILE A 132 -1 N LYS A 130 O PHE A 137 SHEET 1 AA2 4 ARG A 113 CYS A 118 0 SHEET 2 AA2 4 LYS A 185 ARG A 191 -1 O ILE A 190 N ARG A 113 SHEET 3 AA2 4 GLN A 157 ILE A 161 -1 N GLN A 157 O ARG A 191 SHEET 4 AA2 4 GLU A 164 ASN A 165 -1 O GLU A 164 N ILE A 161 SHEET 1 AA3 5 ARG A 197 HIS A 202 0 SHEET 2 AA3 5 VAL A 264 PRO A 271 -1 O ILE A 269 N ARG A 197 SHEET 3 AA3 5 HIS A 236 ILE A 241 -1 N CYS A 239 O THR A 268 SHEET 4 AA3 5 LYS A 217 ILE A 221 -1 N ILE A 218 O HIS A 236 SHEET 5 AA3 5 PHE A 211 LYS A 214 -1 N ILE A 212 O THR A 219 SHEET 1 AA4 4 ARG A 197 HIS A 202 0 SHEET 2 AA4 4 VAL A 264 PRO A 271 -1 O ILE A 269 N ARG A 197 SHEET 3 AA4 4 HIS A 236 ILE A 241 -1 N CYS A 239 O THR A 268 SHEET 4 AA4 4 GLN A 244 ASN A 245 -1 O GLN A 244 N ILE A 241 SHEET 1 AA5 5 ARG B 113 LEU B 117 0 SHEET 2 AA5 5 ILE B 186 ARG B 191 -1 O ILE B 190 N ARG B 113 SHEET 3 AA5 5 GLN B 157 ILE B 161 -1 N GLN B 157 O ARG B 191 SHEET 4 AA5 5 GLY B 135 VAL B 141 -1 N ILE B 136 O VAL B 158 SHEET 5 AA5 5 LEU B 127 ILE B 132 -1 N LYS B 130 O PHE B 137 SHEET 1 AA6 4 ARG B 113 LEU B 117 0 SHEET 2 AA6 4 ILE B 186 ARG B 191 -1 O ILE B 190 N ARG B 113 SHEET 3 AA6 4 GLN B 157 ILE B 161 -1 N GLN B 157 O ARG B 191 SHEET 4 AA6 4 GLU B 164 ASN B 165 -1 O GLU B 164 N ILE B 161 SHEET 1 AA7 5 ARG B 197 HIS B 202 0 SHEET 2 AA7 5 VAL B 264 PRO B 271 -1 O ILE B 269 N ARG B 197 SHEET 3 AA7 5 HIS B 236 ILE B 241 -1 N CYS B 239 O THR B 268 SHEET 4 AA7 5 LYS B 217 ILE B 221 -1 N ILE B 218 O HIS B 236 SHEET 5 AA7 5 PHE B 211 LYS B 214 -1 N ILE B 212 O THR B 219 SHEET 1 AA8 4 ARG B 197 HIS B 202 0 SHEET 2 AA8 4 VAL B 264 PRO B 271 -1 O ILE B 269 N ARG B 197 SHEET 3 AA8 4 HIS B 236 ILE B 241 -1 N CYS B 239 O THR B 268 SHEET 4 AA8 4 GLN B 244 ASN B 245 -1 O GLN B 244 N ILE B 241 SHEET 1 AA9 5 ARG C 113 CYS C 118 0 SHEET 2 AA9 5 LYS C 185 ARG C 191 -1 O ILE C 190 N ARG C 113 SHEET 3 AA9 5 GLN C 157 ILE C 161 -1 N GLN C 157 O ARG C 191 SHEET 4 AA9 5 GLY C 135 VAL C 141 -1 N ILE C 136 O VAL C 158 SHEET 5 AA9 5 LEU C 127 ILE C 132 -1 N LYS C 130 O PHE C 137 SHEET 1 AB1 4 ARG C 113 CYS C 118 0 SHEET 2 AB1 4 LYS C 185 ARG C 191 -1 O ILE C 190 N ARG C 113 SHEET 3 AB1 4 GLN C 157 ILE C 161 -1 N GLN C 157 O ARG C 191 SHEET 4 AB1 4 GLU C 164 ASN C 165 -1 O GLU C 164 N ILE C 161 SHEET 1 AB2 5 ARG C 197 HIS C 202 0 SHEET 2 AB2 5 VAL C 264 PRO C 271 -1 O ILE C 269 N ARG C 197 SHEET 3 AB2 5 HIS C 236 ILE C 241 -1 N CYS C 239 O THR C 268 SHEET 4 AB2 5 LYS C 217 ILE C 221 -1 N ILE C 218 O HIS C 236 SHEET 5 AB2 5 PHE C 211 LYS C 214 -1 N ILE C 212 O THR C 219 SHEET 1 AB3 4 ARG C 197 HIS C 202 0 SHEET 2 AB3 4 VAL C 264 PRO C 271 -1 O ILE C 269 N ARG C 197 SHEET 3 AB3 4 HIS C 236 ILE C 241 -1 N CYS C 239 O THR C 268 SHEET 4 AB3 4 GLN C 244 ASN C 245 -1 O GLN C 244 N ILE C 241 SHEET 1 AB4 5 ARG D 113 CYS D 118 0 SHEET 2 AB4 5 LYS D 185 ARG D 191 -1 O ILE D 190 N ARG D 113 SHEET 3 AB4 5 GLN D 157 ILE D 161 -1 N GLN D 157 O ARG D 191 SHEET 4 AB4 5 GLY D 135 VAL D 141 -1 N ILE D 136 O VAL D 158 SHEET 5 AB4 5 LEU D 127 ILE D 132 -1 N LYS D 130 O PHE D 137 SHEET 1 AB5 4 ARG D 113 CYS D 118 0 SHEET 2 AB5 4 LYS D 185 ARG D 191 -1 O ILE D 190 N ARG D 113 SHEET 3 AB5 4 GLN D 157 ILE D 161 -1 N GLN D 157 O ARG D 191 SHEET 4 AB5 4 GLU D 164 ASN D 165 -1 O GLU D 164 N ILE D 161 SHEET 1 AB6 5 ARG D 197 HIS D 202 0 SHEET 2 AB6 5 VAL D 264 PRO D 271 -1 O ILE D 269 N ARG D 197 SHEET 3 AB6 5 HIS D 236 ILE D 241 -1 N CYS D 239 O THR D 268 SHEET 4 AB6 5 LYS D 217 ILE D 221 -1 N ILE D 218 O HIS D 236 SHEET 5 AB6 5 PHE D 211 LYS D 214 -1 N ILE D 212 O THR D 219 SHEET 1 AB7 4 ARG D 197 HIS D 202 0 SHEET 2 AB7 4 VAL D 264 PRO D 271 -1 O ILE D 269 N ARG D 197 SHEET 3 AB7 4 HIS D 236 ILE D 241 -1 N CYS D 239 O THR D 268 SHEET 4 AB7 4 GLN D 244 ASN D 245 -1 O GLN D 244 N ILE D 241 SITE 1 AC1 5 HIS A 202 SER A 226 ARG A 229 ASN A 230 SITE 2 AC1 5 HOH A 421 SITE 1 AC2 5 ASN A 215 LYS A 250 ASP A 251 HOH A 450 SITE 2 AC2 5 SER D 205 SITE 1 AC3 14 HIS A 208 VAL A 209 GLY A 210 PHE A 211 SITE 2 AC3 14 ILE A 212 PHE A 213 ASP A 251 SER A 252 SITE 3 AC3 14 ALA A 255 LEU A 258 HOH A 406 SER D 259 SITE 4 AC3 14 THR D 260 SER D 261 SITE 1 AC4 3 ILE A 125 GLY A 126 LEU A 127 SITE 1 AC5 5 HIS B 208 VAL B 209 GLY B 210 PHE B 211 SITE 2 AC5 5 HOH B 417 SITE 1 AC6 4 HIS C 202 SER C 226 ARG C 229 ASN C 230 SITE 1 AC7 17 SER B 259 THR B 260 SER B 261 HOH B 423 SITE 2 AC7 17 HIS C 208 VAL C 209 GLY C 210 PHE C 211 SITE 3 AC7 17 ILE C 212 PHE C 213 ASP C 251 SER C 252 SITE 4 AC7 17 ALA C 255 LEU C 258 HOH C 407 HOH C 410 SITE 5 AC7 17 HOH C 458 SITE 1 AC8 4 HIS D 202 SER D 226 ARG D 229 ASN D 230 SITE 1 AC9 5 HIS D 208 VAL D 209 GLY D 210 PHE D 211 SITE 2 AC9 5 HOH D 426 CRYST1 28.937 56.185 100.874 82.59 84.21 78.59 P 1 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 0.034558 -0.006974 -0.002745 0.00000 SCALE2 0.000000 0.018157 -0.002042 0.00000 SCALE3 0.000000 0.000000 0.010027 0.00000