HEADER PROTEIN BINDING 26-FEB-19 6QU9 TITLE FAB FRAGMENT OF AN ANTIBODY THAT INHIBITS POLYMERISATION OF ALPHA-1- TITLE 2 ANTITRYPSIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: FAB 4B12 HEAVY CHAIN; COMPND 3 CHAIN: H, A; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: FAB 4B12 LIGHT CHAIN; COMPND 6 CHAIN: L, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 VARIANT: BALB/C; SOURCE 6 CELL_LINE: HYBRIDOMA; SOURCE 7 ORGAN: SPLEEN; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 10 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 11 ORGANISM_TAXID: 10090; SOURCE 12 VARIANT: BALB/C; SOURCE 13 CELL_LINE: HYBRIDOMA; SOURCE 14 ORGAN: SPLEEN KEYWDS ALPHA-1 ANTITRYPSIN, Z VARIANT, POLYMERS, PROTEIN AGGREGATION, KEYWDS 2 MONOCLONAL ANTIBODY, FAB FRAGMENT, COPD, PROTEASE INHIBITOR, KEYWDS 3 GLYCOPROTEIN, DEFICIENCY, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR A.M.JAGGER,N.HEYER-CHAUHAN,D.A.LOMAS,J.A.IRVING REVDAT 3 01-MAY-24 6QU9 1 REMARK REVDAT 2 04-NOV-20 6QU9 1 JRNL REVDAT 1 18-MAR-20 6QU9 0 JRNL AUTH S.V.FAULL,E.L.K.ELLISTON,B.GOOPTU,A.M.JAGGER,I.ALDOBIYAN, JRNL AUTH 2 A.REDZEJ,M.BADAOUI,N.HEYER-CHAUHAN,S.T.RASHID,G.M.REYNOLDS, JRNL AUTH 3 D.H.ADAMS,E.MIRANDA,E.V.ORLOVA,J.A.IRVING,D.A.LOMAS JRNL TITL THE STRUCTURAL BASIS FOR Z ALPHA 1 -ANTITRYPSIN JRNL TITL 2 POLYMERIZATION IN THE LIVER. JRNL REF SCI ADV V. 6 2020 JRNL REFN ESSN 2375-2548 JRNL PMID 33087346 JRNL DOI 10.1126/SCIADV.ABC1370 REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 63.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 69773 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860 REMARK 3 FREE R VALUE TEST SET COUNT : 3388 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 63.2870 - 5.4794 1.00 2955 152 0.1782 0.1972 REMARK 3 2 5.4794 - 4.3495 1.00 2841 153 0.1482 0.1596 REMARK 3 3 4.3495 - 3.7998 1.00 2857 107 0.1678 0.1844 REMARK 3 4 3.7998 - 3.4524 1.00 2756 164 0.1852 0.2425 REMARK 3 5 3.4524 - 3.2049 1.00 2792 154 0.2090 0.2228 REMARK 3 6 3.2049 - 3.0160 1.00 2753 141 0.2102 0.2812 REMARK 3 7 3.0160 - 2.8649 1.00 2768 162 0.2284 0.2773 REMARK 3 8 2.8649 - 2.7402 1.00 2779 121 0.2351 0.2831 REMARK 3 9 2.7402 - 2.6347 1.00 2728 146 0.2357 0.2635 REMARK 3 10 2.6347 - 2.5438 1.00 2786 153 0.2344 0.2354 REMARK 3 11 2.5438 - 2.4643 1.00 2750 146 0.2372 0.2790 REMARK 3 12 2.4643 - 2.3938 1.00 2705 144 0.2406 0.2533 REMARK 3 13 2.3938 - 2.3308 1.00 2771 151 0.2393 0.2758 REMARK 3 14 2.3308 - 2.2739 1.00 2741 143 0.2395 0.2799 REMARK 3 15 2.2739 - 2.2222 1.00 2746 141 0.2363 0.2752 REMARK 3 16 2.2222 - 2.1749 1.00 2772 130 0.2400 0.2879 REMARK 3 17 2.1749 - 2.1314 1.00 2719 122 0.2481 0.2477 REMARK 3 18 2.1314 - 2.0912 1.00 2758 114 0.2521 0.3197 REMARK 3 19 2.0912 - 2.0539 1.00 2769 119 0.2671 0.2845 REMARK 3 20 2.0539 - 2.0190 1.00 2738 154 0.2628 0.3255 REMARK 3 21 2.0190 - 1.9865 1.00 2685 156 0.2722 0.3292 REMARK 3 22 1.9865 - 1.9559 1.00 2721 139 0.2777 0.3355 REMARK 3 23 1.9559 - 1.9271 1.00 2779 130 0.2874 0.3215 REMARK 3 24 1.9271 - 1.9000 1.00 2716 146 0.2999 0.3167 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 1.00 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.940 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.03 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 : 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 6QU9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1292100854. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 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 : SI(111) REMARK 200 OPTICS : VERTICAL CRL / HORIZONTAL REMARK 200 ELIPTICAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20180126 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.6.2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 69862 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 105.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.84500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.1 REMARK 200 STARTING MODEL: MODEL GENERATED USING ROSETTAANTIBODY PROTOCOL REMARK 200 REMARK 200 REMARK: PLATE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PH 5.5, 25% PEG 3350, REMARK 280 0.2M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 39.63400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.56400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.55100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.56400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.63400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.55100 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 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: 4000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L 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: 3530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 127 REMARK 465 SER A 128 REMARK 465 ALA A 129 REMARK 465 ALA A 130 REMARK 465 ASP A 214 REMARK 465 GLU B 213 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 H 13 CE NZ REMARK 470 LYS H 23 CD CE NZ REMARK 470 HIS H 41 ND1 CD2 CE1 NE2 REMARK 470 VAL H 42 CG1 CG2 REMARK 470 LYS H 43 CG CD CE NZ REMARK 470 GLU H 85 CD OE1 OE2 REMARK 470 LYS H 115 CG CD CE NZ REMARK 470 GLN H 131 CG CD OE1 NE2 REMARK 470 THR H 132 OG1 CG2 REMARK 470 ASN H 133 CG OD1 ND2 REMARK 470 ASP H 173 CG OD1 OD2 REMARK 470 LYS H 205 CD CE NZ REMARK 470 LYS L 24 CD CE NZ REMARK 470 LYS L 39 CE NZ REMARK 470 LYS L 42 CD CE NZ REMARK 470 LYS L 53 CD CE NZ REMARK 470 GLU L 81 CG CD OE1 OE2 REMARK 470 LYS L 103 CE NZ REMARK 470 LYS L 107 CE NZ REMARK 470 LYS L 147 CD CE NZ REMARK 470 LYS L 149 CD CE NZ REMARK 470 GLN L 156 CG CD OE1 NE2 REMARK 470 LYS L 169 CD CE NZ REMARK 470 ASN L 210 CG OD1 ND2 REMARK 470 GLN A 1 CG CD OE1 NE2 REMARK 470 LYS A 13 NZ REMARK 470 LYS A 23 CD CE NZ REMARK 470 HIS A 41 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 43 CD CE NZ REMARK 470 GLN A 61 CG CD OE1 NE2 REMARK 470 GLN A 64 CG CD OE1 NE2 REMARK 470 ASP A 65 CG OD1 OD2 REMARK 470 LYS A 115 CG CD CE NZ REMARK 470 GLN A 131 CG CD OE1 NE2 REMARK 470 ASN A 133 CG OD1 ND2 REMARK 470 ASP A 173 CG OD1 OD2 REMARK 470 LYS A 205 CD CE NZ REMARK 470 LYS A 208 CE NZ REMARK 470 ARG A 213 NE CZ NH1 NH2 REMARK 470 LYS B 24 CG CD CE NZ REMARK 470 LYS B 42 CG CD CE NZ REMARK 470 LYS B 53 CD CE NZ REMARK 470 ASN B 77 CG OD1 ND2 REMARK 470 LYS B 103 CD CE NZ REMARK 470 LYS B 107 CD CE NZ REMARK 470 LYS B 142 CG CD CE NZ REMARK 470 LYS B 147 CG CD CE NZ REMARK 470 LYS B 149 CE NZ REMARK 470 GLN B 156 CD OE1 NE2 REMARK 470 ASN B 157 CG OD1 ND2 REMARK 470 LYS B 169 CD CE NZ REMARK 470 ASP B 184 CG OD1 OD2 REMARK 470 ARG B 188 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 199 CG CD CE NZ REMARK 470 ASN B 212 CG OD1 ND2 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 SER H 44 -134.47 58.74 REMARK 500 PRO H 96 37.55 -91.50 REMARK 500 SER H 172 -102.04 -146.73 REMARK 500 SER H 172 -103.22 -145.96 REMARK 500 THR L 51 -49.36 69.44 REMARK 500 ASP L 93 -65.94 -149.96 REMARK 500 PRO A 96 33.07 -91.15 REMARK 500 SER A 160 -12.93 -140.83 REMARK 500 THR B 51 -51.74 67.85 REMARK 500 ASP B 93 -88.52 -120.97 REMARK 500 ASN B 190 -54.79 -123.26 REMARK 500 ASN B 190 -54.35 -123.53 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 SO4 H 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA L 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-4620 RELATED DB: EMDB REMARK 900 FAB BOUND TO HEAT-INDUCED ALPHA-1-ANTITRYPSIN POLYMER - 3D REMARK 900 RECONSTRUCTION FROM NEGATIVE STAIN REMARK 900 RELATED ID: EMD-4632 RELATED DB: EMDB REMARK 900 FAB BOUND TO PATIENT-DERIVED ALPHA-1-ANTITRYPSIN POLYMER - 3D REMARK 900 RECONSTRUCTION FROM NEGATIVE STAIN REMARK 900 RELATED ID: EMD-4631 RELATED DB: EMDB REMARK 900 FAB BOUND TO PATIENT-DERIVED ALPHA-1-ANTITRYPSIN POLYMER - 3D REMARK 900 RECONSTRUCTION FROM NEGATIVE STAIN DBREF 6QU9 H 1 214 PDB 6QU9 6QU9 1 214 DBREF 6QU9 L 1 213 PDB 6QU9 6QU9 1 213 DBREF 6QU9 A 1 214 PDB 6QU9 6QU9 1 214 DBREF 6QU9 B 1 213 PDB 6QU9 6QU9 1 213 SEQRES 1 H 215 GLN VAL LYS LEU GLU GLU SER GLY PRO GLU LEU VAL LYS SEQRES 2 H 215 PRO GLY ALA SER VAL LYS ILE SER CYS LYS ALA SER GLY SEQRES 3 H 215 TYR SER PHE ILE GLY TYR TYR MET HIS TRP VAL LYS GLN SEQRES 4 H 215 SER HIS VAL LYS SER LEU GLU TRP ILE GLY ARG ILE ASN SEQRES 5 H 215 PRO TYR ASN GLY ALA THR ARG TYR ASN GLN ASN PHE GLN SEQRES 6 H 215 ASP ARG ALA THR LEU THR VAL ASP LYS SER SER SER THR SEQRES 7 H 215 ALA TYR MET ASP PHE HIS SER LEU THR SER GLU ASP SER SEQRES 8 H 215 ALA VAL TYR TYR CYS VAL ARG TRP PRO GLY ASP TYR TRP SEQRES 9 H 215 GLY GLN GLY THR SER VAL THR VAL SER SER ALA LYS THR SEQRES 10 H 215 THR PRO PRO SER VAL TYR PRO LEU ALA PRO GLY SER ALA SEQRES 11 H 215 ALA GLN THR ASN SER MET VAL THR LEU GLY CYS LEU VAL SEQRES 12 H 215 LYS GLY TYR PHE PRO GLU PRO VAL THR VAL THR TRP ASN SEQRES 13 H 215 SER GLY SER LEU SER SER GLY VAL HIS THR PHE PRO ALA SEQRES 14 H 215 VAL LEU GLN SER ASP LEU TYR THR LEU SER SER SER VAL SEQRES 15 H 215 THR VAL PRO SER SER THR TRP PRO SER GLU THR VAL THR SEQRES 16 H 215 CYS ASN VAL ALA HIS PRO ALA SER SER THR LYS VAL ASP SEQRES 17 H 215 LYS LYS ILE VAL PRO ARG ASP SEQRES 1 L 212 ASP ILE VAL MET THR GLN THR PRO SER SER LEU SER ALA SEQRES 2 L 212 SER LEU GLY GLY LYS VAL THR ILE THR CYS LYS ALA SER SEQRES 3 L 212 GLN LYS ILE ASN ASN TYR ILE ALA TRP TYR GLN LEU LYS SEQRES 4 L 212 PRO GLY LYS GLY PRO ARG GLN LEU ILE HIS TYR THR SER SEQRES 5 L 212 LYS LEU GLN PRO GLY ILE PRO SER ARG PHE SER GLY SER SEQRES 6 L 212 GLY SER GLY SER ASP TYR SER PHE SER ILE SER ASN LEU SEQRES 7 L 212 GLU PRO GLU ASP ILE GLY THR TYR TYR CYS LEU ARG TYR SEQRES 8 L 212 GLU ASP LEU TRP THR PHE GLY GLY GLY THR LYS LEU GLU SEQRES 9 L 212 ILE LYS ARG ALA ASP ALA ALA PRO THR VAL SER ILE PHE SEQRES 10 L 212 PRO PRO SER SER GLU GLN LEU THR SER GLY GLY ALA SER SEQRES 11 L 212 VAL VAL CYS PHE LEU ASN ASN PHE TYR PRO LYS ASP ILE SEQRES 12 L 212 ASN VAL LYS TRP LYS ILE ASP GLY SER GLU ARG GLN ASN SEQRES 13 L 212 GLY VAL LEU ASN SER TRP THR ASP GLN ASP SER LYS ASP SEQRES 14 L 212 SER THR TYR SER MET SER SER THR LEU THR LEU THR LYS SEQRES 15 L 212 ASP GLU TYR GLU ARG HIS ASN SER TYR THR CYS GLU ALA SEQRES 16 L 212 THR HIS LYS THR SER THR SER PRO ILE VAL LYS SER PHE SEQRES 17 L 212 ASN ARG ASN GLU SEQRES 1 A 215 GLN VAL LYS LEU GLU GLU SER GLY PRO GLU LEU VAL LYS SEQRES 2 A 215 PRO GLY ALA SER VAL LYS ILE SER CYS LYS ALA SER GLY SEQRES 3 A 215 TYR SER PHE ILE GLY TYR TYR MET HIS TRP VAL LYS GLN SEQRES 4 A 215 SER HIS VAL LYS SER LEU GLU TRP ILE GLY ARG ILE ASN SEQRES 5 A 215 PRO TYR ASN GLY ALA THR ARG TYR ASN GLN ASN PHE GLN SEQRES 6 A 215 ASP ARG ALA THR LEU THR VAL ASP LYS SER SER SER THR SEQRES 7 A 215 ALA TYR MET ASP PHE HIS SER LEU THR SER GLU ASP SER SEQRES 8 A 215 ALA VAL TYR TYR CYS VAL ARG TRP PRO GLY ASP TYR TRP SEQRES 9 A 215 GLY GLN GLY THR SER VAL THR VAL SER SER ALA LYS THR SEQRES 10 A 215 THR PRO PRO SER VAL TYR PRO LEU ALA PRO GLY SER ALA SEQRES 11 A 215 ALA GLN THR ASN SER MET VAL THR LEU GLY CYS LEU VAL SEQRES 12 A 215 LYS GLY TYR PHE PRO GLU PRO VAL THR VAL THR TRP ASN SEQRES 13 A 215 SER GLY SER LEU SER SER GLY VAL HIS THR PHE PRO ALA SEQRES 14 A 215 VAL LEU GLN SER ASP LEU TYR THR LEU SER SER SER VAL SEQRES 15 A 215 THR VAL PRO SER SER THR TRP PRO SER GLU THR VAL THR SEQRES 16 A 215 CYS ASN VAL ALA HIS PRO ALA SER SER THR LYS VAL ASP SEQRES 17 A 215 LYS LYS ILE VAL PRO ARG ASP SEQRES 1 B 212 ASP ILE VAL MET THR GLN THR PRO SER SER LEU SER ALA SEQRES 2 B 212 SER LEU GLY GLY LYS VAL THR ILE THR CYS LYS ALA SER SEQRES 3 B 212 GLN LYS ILE ASN ASN TYR ILE ALA TRP TYR GLN LEU LYS SEQRES 4 B 212 PRO GLY LYS GLY PRO ARG GLN LEU ILE HIS TYR THR SER SEQRES 5 B 212 LYS LEU GLN PRO GLY ILE PRO SER ARG PHE SER GLY SER SEQRES 6 B 212 GLY SER GLY SER ASP TYR SER PHE SER ILE SER ASN LEU SEQRES 7 B 212 GLU PRO GLU ASP ILE GLY THR TYR TYR CYS LEU ARG TYR SEQRES 8 B 212 GLU ASP LEU TRP THR PHE GLY GLY GLY THR LYS LEU GLU SEQRES 9 B 212 ILE LYS ARG ALA ASP ALA ALA PRO THR VAL SER ILE PHE SEQRES 10 B 212 PRO PRO SER SER GLU GLN LEU THR SER GLY GLY ALA SER SEQRES 11 B 212 VAL VAL CYS PHE LEU ASN ASN PHE TYR PRO LYS ASP ILE SEQRES 12 B 212 ASN VAL LYS TRP LYS ILE ASP GLY SER GLU ARG GLN ASN SEQRES 13 B 212 GLY VAL LEU ASN SER TRP THR ASP GLN ASP SER LYS ASP SEQRES 14 B 212 SER THR TYR SER MET SER SER THR LEU THR LEU THR LYS SEQRES 15 B 212 ASP GLU TYR GLU ARG HIS ASN SER TYR THR CYS GLU ALA SEQRES 16 B 212 THR HIS LYS THR SER THR SER PRO ILE VAL LYS SER PHE SEQRES 17 B 212 ASN ARG ASN GLU HET SO4 H 301 5 HET NA L 301 1 HET GOL A 301 6 HET GOL A 302 6 HET SO4 A 303 5 HETNAM SO4 SULFATE ION HETNAM NA SODIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 SO4 2(O4 S 2-) FORMUL 6 NA NA 1+ FORMUL 7 GOL 2(C3 H8 O3) FORMUL 10 HOH *425(H2 O) HELIX 1 AA1 SER H 28 TYR H 32 5 5 HELIX 2 AA2 LYS H 73 SER H 75 5 3 HELIX 3 AA3 THR H 83 SER H 87 5 5 HELIX 4 AA4 SER H 156 SER H 158 5 3 HELIX 5 AA5 PRO H 200 SER H 203 5 4 HELIX 6 AA6 GLU L 79 ILE L 83 5 5 HELIX 7 AA7 SER L 121 SER L 127 1 7 HELIX 8 AA8 LYS L 183 ARG L 188 1 6 HELIX 9 AA9 SER A 28 TYR A 32 5 5 HELIX 10 AB1 THR A 83 SER A 87 5 5 HELIX 11 AB2 SER A 156 SER A 158 5 3 HELIX 12 AB3 PRO A 200 SER A 203 5 4 HELIX 13 AB4 GLU B 79 ILE B 83 5 5 HELIX 14 AB5 SER B 121 SER B 127 1 7 HELIX 15 AB6 LYS B 183 HIS B 189 1 7 SHEET 1 AA1 4 LYS H 3 GLU H 6 0 SHEET 2 AA1 4 VAL H 18 SER H 25 -1 O LYS H 23 N GLU H 5 SHEET 3 AA1 4 THR H 77 PHE H 82 -1 O PHE H 82 N VAL H 18 SHEET 4 AA1 4 ALA H 67 ASP H 72 -1 N ASP H 72 O THR H 77 SHEET 1 AA2 6 GLU H 10 VAL H 12 0 SHEET 2 AA2 6 THR H 107 VAL H 111 1 O SER H 108 N GLU H 10 SHEET 3 AA2 6 ALA H 88 ARG H 94 -1 N ALA H 88 O VAL H 109 SHEET 4 AA2 6 MET H 34 SER H 40 -1 N HIS H 35 O VAL H 93 SHEET 5 AA2 6 SER H 44 ILE H 51 -1 O GLU H 46 N LYS H 38 SHEET 6 AA2 6 THR H 57 TYR H 59 -1 O ARG H 58 N ARG H 50 SHEET 1 AA3 4 SER H 120 LEU H 124 0 SHEET 2 AA3 4 MET H 135 TYR H 145 -1 O GLY H 139 N LEU H 124 SHEET 3 AA3 4 TYR H 175 PRO H 184 -1 O VAL H 181 N LEU H 138 SHEET 4 AA3 4 HIS H 164 THR H 165 -1 N HIS H 164 O SER H 180 SHEET 1 AA4 4 SER H 120 LEU H 124 0 SHEET 2 AA4 4 MET H 135 TYR H 145 -1 O GLY H 139 N LEU H 124 SHEET 3 AA4 4 TYR H 175 PRO H 184 -1 O VAL H 181 N LEU H 138 SHEET 4 AA4 4 VAL H 169 LEU H 170 -1 N VAL H 169 O THR H 176 SHEET 1 AA5 3 THR H 151 TRP H 154 0 SHEET 2 AA5 3 THR H 194 HIS H 199 -1 O ASN H 196 N THR H 153 SHEET 3 AA5 3 THR H 204 LYS H 209 -1 O VAL H 206 N VAL H 197 SHEET 1 AA6 4 MET L 4 THR L 7 0 SHEET 2 AA6 4 VAL L 19 ALA L 25 -1 O THR L 22 N THR L 7 SHEET 3 AA6 4 ASP L 70 ILE L 75 -1 O PHE L 73 N ILE L 21 SHEET 4 AA6 4 PHE L 62 SER L 67 -1 N SER L 63 O SER L 74 SHEET 1 AA7 6 SER L 10 SER L 14 0 SHEET 2 AA7 6 THR L 102 LYS L 107 1 O GLU L 105 N LEU L 11 SHEET 3 AA7 6 GLY L 84 ARG L 90 -1 N GLY L 84 O LEU L 104 SHEET 4 AA7 6 ILE L 33 LEU L 38 -1 N TYR L 36 O TYR L 87 SHEET 5 AA7 6 ARG L 45 HIS L 49 -1 O LEU L 47 N TRP L 35 SHEET 6 AA7 6 LYS L 53 LEU L 54 -1 O LYS L 53 N HIS L 49 SHEET 1 AA8 4 SER L 10 SER L 14 0 SHEET 2 AA8 4 THR L 102 LYS L 107 1 O GLU L 105 N LEU L 11 SHEET 3 AA8 4 GLY L 84 ARG L 90 -1 N GLY L 84 O LEU L 104 SHEET 4 AA8 4 THR L 97 PHE L 98 -1 O THR L 97 N ARG L 90 SHEET 1 AA9 4 THR L 114 PHE L 118 0 SHEET 2 AA9 4 GLY L 129 PHE L 139 -1 O PHE L 135 N SER L 116 SHEET 3 AA9 4 TYR L 173 THR L 182 -1 O LEU L 179 N VAL L 132 SHEET 4 AA9 4 VAL L 159 TRP L 163 -1 N LEU L 160 O THR L 178 SHEET 1 AB1 4 SER L 153 ARG L 155 0 SHEET 2 AB1 4 ILE L 144 ILE L 150 -1 N ILE L 150 O SER L 153 SHEET 3 AB1 4 SER L 191 HIS L 198 -1 O THR L 193 N LYS L 149 SHEET 4 AB1 4 ILE L 205 ASN L 210 -1 O LYS L 207 N CYS L 194 SHEET 1 AB2 4 LYS A 3 GLU A 6 0 SHEET 2 AB2 4 VAL A 18 SER A 25 -1 O LYS A 23 N GLU A 5 SHEET 3 AB2 4 THR A 77 PHE A 82 -1 O ALA A 78 N CYS A 22 SHEET 4 AB2 4 ALA A 67 ASP A 72 -1 N THR A 68 O ASP A 81 SHEET 1 AB3 6 GLU A 10 VAL A 12 0 SHEET 2 AB3 6 THR A 107 VAL A 111 1 O SER A 108 N GLU A 10 SHEET 3 AB3 6 ALA A 88 ARG A 94 -1 N ALA A 88 O VAL A 109 SHEET 4 AB3 6 MET A 34 GLN A 39 -1 N HIS A 35 O VAL A 93 SHEET 5 AB3 6 LEU A 45 ILE A 51 -1 O GLU A 46 N LYS A 38 SHEET 6 AB3 6 THR A 57 TYR A 59 -1 O ARG A 58 N ARG A 50 SHEET 1 AB4 4 GLU A 10 VAL A 12 0 SHEET 2 AB4 4 THR A 107 VAL A 111 1 O SER A 108 N GLU A 10 SHEET 3 AB4 4 ALA A 88 ARG A 94 -1 N ALA A 88 O VAL A 109 SHEET 4 AB4 4 TYR A 102 TRP A 103 -1 O TYR A 102 N ARG A 94 SHEET 1 AB5 4 SER A 120 LEU A 124 0 SHEET 2 AB5 4 MET A 135 TYR A 145 -1 O LEU A 141 N TYR A 122 SHEET 3 AB5 4 LEU A 174 PRO A 184 -1 O TYR A 175 N TYR A 145 SHEET 4 AB5 4 VAL A 163 THR A 165 -1 N HIS A 164 O SER A 180 SHEET 1 AB6 4 SER A 120 LEU A 124 0 SHEET 2 AB6 4 MET A 135 TYR A 145 -1 O LEU A 141 N TYR A 122 SHEET 3 AB6 4 LEU A 174 PRO A 184 -1 O TYR A 175 N TYR A 145 SHEET 4 AB6 4 VAL A 169 GLN A 171 -1 N GLN A 171 O LEU A 174 SHEET 1 AB7 3 THR A 151 TRP A 154 0 SHEET 2 AB7 3 THR A 194 HIS A 199 -1 O ASN A 196 N THR A 153 SHEET 3 AB7 3 THR A 204 LYS A 209 -1 O VAL A 206 N VAL A 197 SHEET 1 AB8 4 MET B 4 THR B 7 0 SHEET 2 AB8 4 LYS B 18 ALA B 25 -1 O LYS B 24 N THR B 5 SHEET 3 AB8 4 ASP B 70 SER B 76 -1 O PHE B 73 N ILE B 21 SHEET 4 AB8 4 PHE B 62 SER B 67 -1 N SER B 63 O SER B 74 SHEET 1 AB9 6 SER B 10 SER B 14 0 SHEET 2 AB9 6 THR B 102 LYS B 107 1 O LYS B 107 N ALA B 13 SHEET 3 AB9 6 GLY B 84 ARG B 90 -1 N GLY B 84 O LEU B 104 SHEET 4 AB9 6 ILE B 33 LEU B 38 -1 N LEU B 38 O THR B 85 SHEET 5 AB9 6 ARG B 45 HIS B 49 -1 O LEU B 47 N TRP B 35 SHEET 6 AB9 6 LYS B 53 LEU B 54 -1 O LYS B 53 N HIS B 49 SHEET 1 AC1 4 SER B 10 SER B 14 0 SHEET 2 AC1 4 THR B 102 LYS B 107 1 O LYS B 107 N ALA B 13 SHEET 3 AC1 4 GLY B 84 ARG B 90 -1 N GLY B 84 O LEU B 104 SHEET 4 AC1 4 THR B 97 PHE B 98 -1 O THR B 97 N ARG B 90 SHEET 1 AC2 4 THR B 114 PHE B 118 0 SHEET 2 AC2 4 GLY B 129 PHE B 139 -1 O PHE B 135 N SER B 116 SHEET 3 AC2 4 TYR B 173 THR B 182 -1 O LEU B 181 N ALA B 130 SHEET 4 AC2 4 VAL B 159 TRP B 163 -1 N LEU B 160 O THR B 178 SHEET 1 AC3 4 SER B 153 ARG B 155 0 SHEET 2 AC3 4 ASN B 145 ILE B 150 -1 N TRP B 148 O ARG B 155 SHEET 3 AC3 4 SER B 191 THR B 197 -1 O THR B 197 N ASN B 145 SHEET 4 AC3 4 ILE B 205 ASN B 210 -1 O LYS B 207 N CYS B 194 SSBOND 1 CYS H 22 CYS H 92 1555 1555 2.03 SSBOND 2 CYS H 140 CYS H 195 1555 1555 2.04 SSBOND 3 CYS L 23 CYS L 88 1555 1555 2.06 SSBOND 4 CYS L 134 CYS L 194 1555 1555 2.03 SSBOND 5 CYS A 22 CYS A 92 1555 1555 2.03 SSBOND 6 CYS A 140 CYS A 195 1555 1555 2.04 SSBOND 7 CYS B 23 CYS B 88 1555 1555 2.07 SSBOND 8 CYS B 134 CYS B 194 1555 1555 2.03 LINK OG SER L 65 NA NA L 301 1555 1555 3.19 CISPEP 1 TRP H 95 PRO H 96 0 7.44 CISPEP 2 PHE H 146 PRO H 147 0 -4.96 CISPEP 3 GLU H 148 PRO H 149 0 -0.33 CISPEP 4 TRP H 188 PRO H 189 0 7.60 CISPEP 5 THR L 7 PRO L 8 0 -5.68 CISPEP 6 TYR L 140 PRO L 141 0 1.64 CISPEP 7 TRP A 95 PRO A 96 0 3.49 CISPEP 8 PHE A 146 PRO A 147 0 -3.69 CISPEP 9 GLU A 148 PRO A 149 0 -0.55 CISPEP 10 TRP A 188 PRO A 189 0 5.82 CISPEP 11 THR B 7 PRO B 8 0 -0.64 CISPEP 12 TYR B 140 PRO B 141 0 4.47 SITE 1 AC1 8 HOH A 441 ARG H 50 ALA H 56 ARG H 58 SITE 2 AC1 8 HOH H 415 HOH H 426 HOH H 433 HOH H 446 SITE 1 AC2 3 SER L 63 GLY L 64 SER L 65 SITE 1 AC3 5 GLU A 191 THR A 192 HOH A 404 HOH A 405 SITE 2 AC3 5 HOH L 424 SITE 1 AC4 6 GLU A 148 PRO A 149 VAL A 150 ALA A 168 SITE 2 AC4 6 LEU A 177 HOH A 465 SITE 1 AC5 7 TYR A 33 ASN A 52 ASN A 54 HOH A 403 SITE 2 AC5 7 HOH A 420 HOH A 467 LYS L 183 CRYST1 79.268 105.102 105.128 90.00 90.00 90.00 P 21 21 21 8 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 0.012615 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009515 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009512 0.00000