HEADER MEMBRANE PROTEIN 01-SEP-16 5GV3 TITLE CRYSTAL STRUCTURE OF THE MEMBRANE-DISTAL DOMAIN OF MOUSE LYSOSOME- TITLE 2 ASSOCIATED MEMBRANE PROTEIN 2 (LAMP-2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOSOME-ASSOCIATED MEMBRANE GLYCOPROTEIN 2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 26-189; COMPND 5 SYNONYM: LYSOSOME-ASSOCIATED MEMBRANE PROTEIN 2,CD107 ANTIGEN-LIKE COMPND 6 FAMILY MEMBER B,LYSOSOMAL MEMBRANE GLYCOPROTEIN TYPE B,LGP-B; COMPND 7 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: LAMP2, LAMP-2; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PORIP KEYWDS MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.TOMABECHI,H.EHARA,M.KUKIMOTO-NIINO,M.SHIROUZU REVDAT 4 09-OCT-24 5GV3 1 REMARK HETSYN REVDAT 3 29-JUL-20 5GV3 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 20-MAR-19 5GV3 1 JRNL REVDAT 1 06-SEP-17 5GV3 0 JRNL AUTH K.TERASAWA,Y.TOMABECHI,M.IKEDA,H.EHARA,M.KUKIMOTO-NIINO, JRNL AUTH 2 M.WAKIYAMA,K.A.PODYMA-INOUE,A.R.RAJAPAKSHE,T.WATABE, JRNL AUTH 3 M.SHIROUZU,M.HARA-YOKOYAMA JRNL TITL LYSOSOME-ASSOCIATED MEMBRANE PROTEINS-1 AND -2 (LAMP-1 AND JRNL TITL 2 LAMP-2) ASSEMBLE VIA DISTINCT MODES. JRNL REF BIOCHEM. BIOPHYS. RES. V. 479 489 2016 JRNL REF 2 COMMUN. JRNL REFN ESSN 1090-2104 JRNL PMID 27663661 JRNL DOI 10.1016/J.BBRC.2016.09.093 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1690 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 23657 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.272 REMARK 3 R VALUE (WORKING SET) : 0.269 REMARK 3 FREE R VALUE : 0.308 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.370 REMARK 3 FREE R VALUE TEST SET COUNT : 1979 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 40.4956 - 5.0498 0.99 1668 146 0.2695 0.2989 REMARK 3 2 5.0498 - 4.0093 1.00 1590 147 0.2298 0.2578 REMARK 3 3 4.0093 - 3.5028 1.00 1578 148 0.2477 0.2792 REMARK 3 4 3.5028 - 3.1827 1.00 1567 145 0.2627 0.2862 REMARK 3 5 3.1827 - 2.9547 0.99 1551 137 0.2897 0.3459 REMARK 3 6 2.9547 - 2.7805 0.99 1570 141 0.2826 0.3853 REMARK 3 7 2.7805 - 2.6413 0.99 1533 144 0.3184 0.3259 REMARK 3 8 2.6413 - 2.5263 0.99 1537 143 0.3018 0.3701 REMARK 3 9 2.5263 - 2.4291 0.99 1540 143 0.2982 0.3434 REMARK 3 10 2.4291 - 2.3453 0.99 1514 143 0.2860 0.3803 REMARK 3 11 2.3453 - 2.2719 0.99 1533 137 0.2985 0.3448 REMARK 3 12 2.2719 - 2.2070 0.99 1521 133 0.3168 0.3568 REMARK 3 13 2.2070 - 2.1489 0.98 1502 140 0.3108 0.4014 REMARK 3 14 2.1489 - 2.0965 0.94 1474 132 0.3463 0.3749 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) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.700 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 2821 REMARK 3 ANGLE : 1.342 3754 REMARK 3 CHIRALITY : 0.061 463 REMARK 3 PLANARITY : 0.006 468 REMARK 3 DIHEDRAL : 11.610 940 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 : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A REMARK 3 SELECTION : CHAIN B REMARK 3 ATOM PAIRS NUMBER : 1428 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5GV3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1300001510. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-OCT-14 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 : SPRING-8 REMARK 200 BEAMLINE : BL26B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23657 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.096 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 (%) : 98.7 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06800 REMARK 200 FOR THE DATA SET : 16.3100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15 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: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM ZINC ACETATE, 20% (V/V) REMARK 280 POLYETHYLENE GLYCOL 3500, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.59000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 64.59000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 29.80500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.96500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 29.80500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.96500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 64.59000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 29.80500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 51.96500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 64.59000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 29.80500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 51.96500 REMARK 290 SMTRY3 8 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: MONOMERIC 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 327 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 328 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 76 REMARK 465 ASP A 77 REMARK 465 ASP A 78 REMARK 465 ARG A 79 REMARK 465 GLY A 190 REMARK 465 SER A 191 REMARK 465 SER A 192 REMARK 465 LEU A 193 REMARK 465 ASP B 188 REMARK 465 GLN B 189 REMARK 465 GLY B 190 REMARK 465 SER B 191 REMARK 465 SER B 192 REMARK 465 LEU B 193 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 O HOH A 328 O HOH A 343 1.35 REMARK 500 O HOH A 339 O HOH A 343 1.46 REMARK 500 O HOH A 301 O HOH A 319 1.54 REMARK 500 ND1 HIS A 131 O HOH A 301 1.57 REMARK 500 CE1 HIS B 108 O HOH B 302 1.70 REMARK 500 NZ LYS B 148 OE1 GLU B 182 1.72 REMARK 500 OD1 ASP A 118 OG1 THR A 120 1.82 REMARK 500 NE2 HIS B 70 O HOH B 301 1.84 REMARK 500 OG SER A 151 OD1 ASP A 188 2.07 REMARK 500 O HOH B 308 O HOH B 326 2.08 REMARK 500 OD1 ASP B 109 O HOH B 302 2.11 REMARK 500 OE2 GLU B 101 NZ LYS B 140 2.14 REMARK 500 OE1 GLU B 43 O HOH B 303 2.14 REMARK 500 OD1 ASN B 150 O HOH B 304 2.15 REMARK 500 OE1 GLU A 186 O HOH A 302 2.17 REMARK 500 ND1 HIS B 108 O HOH B 302 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE2 GLU A 41 ZN ZN B 206 4566 1.63 REMARK 500 ND2 ASN A 150 OE2 GLU B 41 4566 2.07 REMARK 500 O HOH A 335 O HOH B 312 4566 2.10 REMARK 500 OD1 ASN A 150 OD2 ASP B 25 4566 2.16 REMARK 500 OE2 GLU B 101 ND1 HIS B 131 8566 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU B 43 CB GLU B 43 CG 0.223 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 ASP A 32 -163.44 -118.49 REMARK 500 LYS A 67 -29.20 147.26 REMARK 500 SER A 81 62.58 77.41 REMARK 500 ALA A 82 118.95 -15.75 REMARK 500 GLU A 101 41.19 71.05 REMARK 500 SER A 103 72.85 110.46 REMARK 500 PHE A 122 68.39 -117.66 REMARK 500 CYS A 149 87.93 -158.11 REMARK 500 LEU A 157 72.44 -119.05 REMARK 500 ASN A 175 18.21 58.79 REMARK 500 ASP B 32 -169.79 -123.22 REMARK 500 ASP B 77 -161.47 -117.23 REMARK 500 PHE B 90 -149.26 -106.84 REMARK 500 GLU B 101 -147.29 -109.93 REMARK 500 SER B 103 -47.76 -144.85 REMARK 500 ASN B 175 16.78 57.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS B 67 ALA B 68 142.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 ZN A 204 REMARK 615 ZN A 205 REMARK 615 ZN A 209 REMARK 615 ZN B 205 REMARK 615 ZN B 206 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 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 41 OE1 REMARK 620 2 GLU A 41 OE2 64.3 REMARK 620 3 HOH A 323 O 85.4 149.3 REMARK 620 4 GLU B 43 OE2 109.3 47.4 162.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 43 OE1 REMARK 620 2 GLU A 43 OE2 66.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 70 NE2 REMARK 620 2 HOH A 311 O 76.6 REMARK 620 3 HOH A 328 O 90.3 166.1 REMARK 620 4 HOH A 339 O 104.6 111.6 76.0 REMARK 620 5 HOH A 343 O 109.7 152.2 37.8 40.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 205 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 118 OD1 REMARK 620 2 ASP A 118 OD2 66.2 REMARK 620 3 THR A 120 OG1 53.5 78.0 REMARK 620 4 HOH A 305 O 123.4 70.0 84.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 204 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 131 ND1 REMARK 620 2 HIS A 131 NE2 63.4 REMARK 620 3 HOH A 301 O 44.5 99.6 REMARK 620 4 HOH A 319 O 83.4 112.6 43.2 REMARK 620 5 HOH A 345 O 154.6 111.2 119.0 76.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 150 OD1 REMARK 620 2 ASN A 150 ND2 64.7 REMARK 620 3 ASP B 25 OD2 102.0 76.5 REMARK 620 4 GLU B 41 OE2 95.7 74.1 6.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 182 OE1 REMARK 620 2 GLU A 182 OE2 64.0 REMARK 620 3 LYS B 148 NZ 113.3 156.5 REMARK 620 4 HIS B 168 NE2 112.4 158.7 2.6 REMARK 620 5 GLU B 182 OE1 115.1 156.0 2.0 4.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 206 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 43 OE1 REMARK 620 2 GLU B 43 OE2 67.6 REMARK 620 3 HOH B 303 O 63.1 74.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 51 OE1 REMARK 620 2 GLU B 51 OE2 64.8 REMARK 620 3 HIS B 108 ND1 52.0 116.7 REMARK 620 4 HIS B 108 NE2 55.7 120.4 3.7 REMARK 620 5 ASP B 109 OD1 54.7 119.3 5.7 5.1 REMARK 620 6 ASP B 109 OD2 54.0 118.5 7.4 7.3 2.3 REMARK 620 7 HOH B 302 O 54.8 119.6 3.0 1.1 4.3 6.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 204 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 70 NE2 REMARK 620 2 HOH B 301 O 52.8 REMARK 620 3 HOH B 327 O 112.5 98.6 REMARK 620 4 HOH B 327 O 111.3 97.9 1.2 REMARK 620 5 HOH B 328 O 111.8 98.8 1.0 0.9 REMARK 620 6 HOH B 328 O 111.8 98.8 1.0 0.9 0.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 205 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 70 NE2 REMARK 620 2 HOH B 301 O 52.8 REMARK 620 3 HOH B 316 O 84.0 78.5 REMARK 620 4 HOH B 327 O 112.2 98.1 157.2 REMARK 620 5 HOH B 327 O 114.4 100.0 156.1 2.3 REMARK 620 6 HOH B 328 O 113.1 99.5 157.3 1.4 1.4 REMARK 620 7 HOH B 328 O 113.1 99.5 157.3 1.4 1.4 0.0 REMARK 620 N 1 2 3 4 5 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5GV0 RELATED DB: PDB DBREF 5GV3 A 26 189 UNP P17047 LAMP2_MOUSE 26 189 DBREF 5GV3 B 26 189 UNP P17047 LAMP2_MOUSE 26 189 SEQADV 5GV3 ASP A 25 UNP P17047 EXPRESSION TAG SEQADV 5GV3 GLY A 190 UNP P17047 EXPRESSION TAG SEQADV 5GV3 SER A 191 UNP P17047 EXPRESSION TAG SEQADV 5GV3 SER A 192 UNP P17047 EXPRESSION TAG SEQADV 5GV3 LEU A 193 UNP P17047 EXPRESSION TAG SEQADV 5GV3 ASP B 25 UNP P17047 EXPRESSION TAG SEQADV 5GV3 GLY B 190 UNP P17047 EXPRESSION TAG SEQADV 5GV3 SER B 191 UNP P17047 EXPRESSION TAG SEQADV 5GV3 SER B 192 UNP P17047 EXPRESSION TAG SEQADV 5GV3 LEU B 193 UNP P17047 EXPRESSION TAG SEQRES 1 A 169 ASP LEU ILE VAL ASN LEU THR ASP SER LYS GLY THR CYS SEQRES 2 A 169 LEU TYR ALA GLU TRP GLU MET ASN PHE THR ILE THR TYR SEQRES 3 A 169 GLU THR THR ASN GLN THR ASN LYS THR ILE THR ILE ALA SEQRES 4 A 169 VAL PRO ASP LYS ALA THR HIS ASP GLY SER SER CYS GLY SEQRES 5 A 169 ASP ASP ARG ASN SER ALA LYS ILE MET ILE GLN PHE GLY SEQRES 6 A 169 PHE ALA VAL SER TRP ALA VAL ASN PHE THR LYS GLU ALA SEQRES 7 A 169 SER HIS TYR SER ILE HIS ASP ILE VAL LEU SER TYR ASN SEQRES 8 A 169 THR SER ASP SER THR VAL PHE PRO GLY ALA VAL ALA LYS SEQRES 9 A 169 GLY VAL HIS THR VAL LYS ASN PRO GLU ASN PHE LYS VAL SEQRES 10 A 169 PRO LEU ASP VAL ILE PHE LYS CYS ASN SER VAL LEU THR SEQRES 11 A 169 TYR ASN LEU THR PRO VAL VAL GLN LYS TYR TRP GLY ILE SEQRES 12 A 169 HIS LEU GLN ALA PHE VAL GLN ASN GLY THR VAL SER LYS SEQRES 13 A 169 ASN GLU GLN VAL CYS GLU GLU ASP GLN GLY SER SER LEU SEQRES 1 B 169 ASP LEU ILE VAL ASN LEU THR ASP SER LYS GLY THR CYS SEQRES 2 B 169 LEU TYR ALA GLU TRP GLU MET ASN PHE THR ILE THR TYR SEQRES 3 B 169 GLU THR THR ASN GLN THR ASN LYS THR ILE THR ILE ALA SEQRES 4 B 169 VAL PRO ASP LYS ALA THR HIS ASP GLY SER SER CYS GLY SEQRES 5 B 169 ASP ASP ARG ASN SER ALA LYS ILE MET ILE GLN PHE GLY SEQRES 6 B 169 PHE ALA VAL SER TRP ALA VAL ASN PHE THR LYS GLU ALA SEQRES 7 B 169 SER HIS TYR SER ILE HIS ASP ILE VAL LEU SER TYR ASN SEQRES 8 B 169 THR SER ASP SER THR VAL PHE PRO GLY ALA VAL ALA LYS SEQRES 9 B 169 GLY VAL HIS THR VAL LYS ASN PRO GLU ASN PHE LYS VAL SEQRES 10 B 169 PRO LEU ASP VAL ILE PHE LYS CYS ASN SER VAL LEU THR SEQRES 11 B 169 TYR ASN LEU THR PRO VAL VAL GLN LYS TYR TRP GLY ILE SEQRES 12 B 169 HIS LEU GLN ALA PHE VAL GLN ASN GLY THR VAL SER LYS SEQRES 13 B 169 ASN GLU GLN VAL CYS GLU GLU ASP GLN GLY SER SER LEU HET ZN A 201 1 HET ZN A 202 1 HET ZN A 203 1 HET ZN A 204 1 HET ZN A 205 1 HET ZN A 206 1 HET ZN A 207 1 HET ZN A 208 1 HET ZN A 209 1 HET NAG A 210 14 HET NAG A 211 14 HET NAG A 212 14 HET NAG A 213 14 HET NAG A 214 14 HET ZN B 201 1 HET ZN B 202 1 HET ZN B 203 1 HET ZN B 204 1 HET ZN B 205 1 HET ZN B 206 1 HET NAG B 207 14 HET NAG B 208 14 HET NAG B 209 14 HET NAG B 210 14 HET NAG B 211 14 HETNAM ZN ZINC ION HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 3 ZN 15(ZN 2+) FORMUL 12 NAG 10(C8 H15 N O6) FORMUL 28 HOH *82(H2 O) HELIX 1 AA1 GLU A 186 GLN A 189 5 4 SHEET 1 AA1 4 LEU A 26 ASP A 32 0 SHEET 2 AA1 4 GLY A 35 THR A 52 -1 O ALA A 40 N VAL A 28 SHEET 3 AA1 4 VAL A 160 GLN A 170 -1 O HIS A 168 N GLU A 41 SHEET 4 AA1 4 LEU A 153 LEU A 157 -1 N LEU A 153 O TYR A 164 SHEET 1 AA2 5 THR A 56 ALA A 63 0 SHEET 2 AA2 5 GLY A 35 THR A 52 -1 N THR A 52 O THR A 56 SHEET 3 AA2 5 VAL A 160 GLN A 170 -1 O HIS A 168 N GLU A 41 SHEET 4 AA2 5 ILE A 146 CYS A 149 -1 N PHE A 147 O LEU A 169 SHEET 5 AA2 5 GLU A 182 VAL A 184 1 O GLN A 183 N LYS A 148 SHEET 1 AA3 4 LYS A 83 PHE A 88 0 SHEET 2 AA3 4 VAL A 92 LYS A 100 -1 O TRP A 94 N ILE A 86 SHEET 3 AA3 4 TYR A 105 ASN A 115 -1 O HIS A 108 N ASN A 97 SHEET 4 AA3 4 VAL A 130 LYS A 134 -1 O HIS A 131 N TYR A 114 SHEET 1 AA4 4 LYS A 83 PHE A 88 0 SHEET 2 AA4 4 VAL A 92 LYS A 100 -1 O TRP A 94 N ILE A 86 SHEET 3 AA4 4 TYR A 105 ASN A 115 -1 O HIS A 108 N ASN A 97 SHEET 4 AA4 4 PHE A 139 VAL A 141 -1 O PHE A 139 N ILE A 107 SHEET 1 AA5 4 LEU B 26 ASP B 32 0 SHEET 2 AA5 4 GLY B 35 GLU B 51 -1 O GLY B 35 N ASP B 32 SHEET 3 AA5 4 VAL B 160 GLN B 170 -1 O TRP B 165 N GLU B 43 SHEET 4 AA5 4 LEU B 153 LEU B 157 -1 N LEU B 153 O TYR B 164 SHEET 1 AA6 5 ASN B 57 ALA B 63 0 SHEET 2 AA6 5 GLY B 35 GLU B 51 -1 N PHE B 46 O ILE B 62 SHEET 3 AA6 5 VAL B 160 GLN B 170 -1 O TRP B 165 N GLU B 43 SHEET 4 AA6 5 ILE B 146 CYS B 149 -1 N PHE B 147 O LEU B 169 SHEET 5 AA6 5 GLU B 182 VAL B 184 1 O GLN B 183 N LYS B 148 SHEET 1 AA7 4 ALA B 82 GLN B 87 0 SHEET 2 AA7 4 VAL B 92 LYS B 100 -1 O TRP B 94 N ILE B 86 SHEET 3 AA7 4 HIS B 104 ASN B 115 -1 O SER B 113 N SER B 93 SHEET 4 AA7 4 VAL B 130 LYS B 134 -1 O HIS B 131 N TYR B 114 SHEET 1 AA8 4 ALA B 82 GLN B 87 0 SHEET 2 AA8 4 VAL B 92 LYS B 100 -1 O TRP B 94 N ILE B 86 SHEET 3 AA8 4 HIS B 104 ASN B 115 -1 O SER B 113 N SER B 93 SHEET 4 AA8 4 PHE B 139 PRO B 142 -1 O PHE B 139 N ILE B 107 SSBOND 1 CYS A 37 CYS A 75 1555 1555 2.04 SSBOND 2 CYS A 149 CYS A 185 1555 1555 2.05 SSBOND 3 CYS B 37 CYS B 75 1555 1555 2.03 SSBOND 4 CYS B 149 CYS B 185 1555 1555 2.05 LINK ND2 ASN A 29 C1 NAG A 210 1555 1555 1.43 LINK ND2 ASN A 45 C1 NAG A 211 1555 1555 1.45 LINK ND2 ASN A 57 C1 NAG A 214 1555 1555 1.44 LINK ND2 ASN A 97 C1 NAG A 213 1555 1555 1.43 LINK ND2 ASN A 115 C1 NAG A 212 1555 1555 1.44 LINK ND2 ASN B 29 C1 NAG B 207 1555 1555 1.44 LINK ND2 ASN B 45 C1 NAG B 211 1555 1555 1.43 LINK ND2 ASN B 57 C1 NAG B 210 1555 1555 1.44 LINK ND2 ASN B 97 C1 NAG B 209 1555 1555 1.44 LINK ND2 ASN B 115 C1 NAG B 208 1555 1555 1.44 LINK OE1 GLU A 41 ZN ZN A 201 1555 1555 2.00 LINK OE2 GLU A 41 ZN ZN A 201 1555 1555 2.03 LINK OE1 GLU A 43 ZN ZN A 203 1555 1555 2.00 LINK OE2 GLU A 43 ZN ZN A 203 1555 1555 2.00 LINK NE2 HIS A 70 ZN ZN A 202 1555 1555 2.01 LINK OD1 ASP A 118 ZN ZN A 205 1555 1555 1.99 LINK OD2 ASP A 118 ZN ZN A 205 1555 1555 2.00 LINK OG1 THR A 120 ZN ZN A 205 1555 1555 2.05 LINK ND1 HIS A 131 ZN ZN A 204 1555 1555 2.03 LINK NE2 HIS A 131 ZN ZN A 204 1555 1555 2.04 LINK OD1 ASN A 150 ZN ZN B 203 1555 4566 2.06 LINK ND2 ASN A 150 ZN ZN B 203 1555 4566 2.07 LINK OE1 GLU A 182 ZN ZN B 202 1555 4566 2.05 LINK OE2 GLU A 182 ZN ZN B 202 1555 4566 2.00 LINK ZN ZN A 201 O HOH A 323 1555 1555 2.09 LINK ZN ZN A 201 OE2 GLU B 43 4566 1555 1.98 LINK ZN ZN A 202 O HOH A 311 1555 1555 2.10 LINK ZN ZN A 202 O HOH A 328 1555 1555 2.09 LINK ZN ZN A 202 O HOH A 339 1555 1555 2.09 LINK ZN ZN A 202 O HOH A 343 1555 1555 2.09 LINK ZN ZN A 204 O HOH A 301 1555 1555 2.10 LINK ZN ZN A 204 O HOH A 319 1555 1555 2.09 LINK ZN ZN A 204 O HOH A 345 1555 1555 2.10 LINK ZN ZN A 205 O HOH A 305 1555 1555 2.09 LINK OD2 ASP B 25 ZN ZN B 203 1555 1555 2.01 LINK OE2 GLU B 41 ZN ZN B 203 1555 1555 2.00 LINK OE1 GLU B 43 ZN ZN B 206 1555 1555 2.00 LINK OE2 GLU B 43 ZN ZN B 206 1555 1555 1.98 LINK OE1 GLU B 51 ZN ZN B 201 1555 8466 2.02 LINK OE2 GLU B 51 ZN ZN B 201 1555 8466 2.02 LINK NE2 HIS B 70 ZN ZN B 204 1555 1555 2.05 LINK NE2 HIS B 70 ZN ZN B 205 1555 1555 2.05 LINK ND1 HIS B 108 ZN ZN B 201 1555 1555 2.44 LINK NE2 HIS B 108 ZN ZN B 201 1555 1555 2.03 LINK OD1 ASP B 109 ZN ZN B 201 1555 1555 2.00 LINK OD2 ASP B 109 ZN ZN B 201 1555 1555 2.02 LINK NZ LYS B 148 ZN ZN B 202 1555 1555 2.04 LINK NE2 HIS B 168 ZN ZN B 202 1555 1555 2.05 LINK OE1 GLU B 182 ZN ZN B 202 1555 1555 2.03 LINK ZN ZN B 201 O HOH B 302 1555 1555 2.09 LINK ZN ZN B 204 O HOH B 301 1555 1555 2.09 LINK ZN ZN B 204 O HOH B 327 1555 1555 2.09 LINK ZN ZN B 204 O HOH B 327 1555 4566 2.16 LINK ZN ZN B 204 O HOH B 328 1555 1555 2.13 LINK ZN ZN B 204 O HOH B 328 1555 4566 2.13 LINK ZN ZN B 205 O HOH B 301 1555 1555 2.09 LINK ZN ZN B 205 O HOH B 316 1555 1555 2.09 LINK ZN ZN B 205 O HOH B 327 1555 1555 2.10 LINK ZN ZN B 205 O HOH B 327 1555 4566 2.09 LINK ZN ZN B 205 O HOH B 328 1555 1555 2.10 LINK ZN ZN B 205 O HOH B 328 1555 4566 2.10 LINK ZN ZN B 206 O HOH B 303 1555 1555 2.10 CISPEP 1 SER A 103 HIS A 104 0 -8.42 CISPEP 2 THR A 158 PRO A 159 0 5.69 CISPEP 3 SER B 33 LYS B 34 0 2.10 CISPEP 4 ASP B 66 LYS B 67 0 -3.60 CISPEP 5 LYS B 128 GLY B 129 0 -7.10 CISPEP 6 THR B 158 PRO B 159 0 7.06 CRYST1 59.610 103.930 129.180 90.00 90.00 90.00 C 2 2 21 16 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016776 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009622 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007741 0.00000