HEADER HYDROLASE 15-MAY-08 3D4Z TITLE GOLGI MANNOSIDASE II COMPLEX WITH GLUCO-IMIDAZOLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-MANNOSIDASE 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; UNP RESIDUES 76-1108; COMPND 5 SYNONYM: ALPHA-MANNOSIDASE II, MANNOSYL-OLIGOSACCHARIDE 1,3-1,6- COMPND 6 ALPHA-MANNOSIDASE, MAN II, GOLGI ALPHA-MANNOSIDASE II, AMAN II; COMPND 7 EC: 3.2.1.114; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 GENE: ALPHA-MAN-II, GMII; SOURCE 5 EXPRESSION_SYSTEM: DROSOPHILA MELANOGASTER; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: S2 CELLS; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PMTBIP_NHIS KEYWDS GH38 GLYCOSIDASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.A.KUNTZ,C.A.TARLING,S.G.WITHERS,D.R.ROSE REVDAT 5 30-OCT-24 3D4Z 1 REMARK SEQADV REVDAT 4 24-JUL-19 3D4Z 1 REMARK REVDAT 3 24-FEB-09 3D4Z 1 VERSN REVDAT 2 07-OCT-08 3D4Z 1 JRNL REVDAT 1 05-AUG-08 3D4Z 0 JRNL AUTH D.A.KUNTZ,C.A.TARLING,S.G.WITHERS,D.R.ROSE JRNL TITL STRUCTURAL ANALYSIS OF GOLGI ALPHA-MANNOSIDASE II INHIBITORS JRNL TITL 2 IDENTIFIED FROM A FOCUSED GLYCOSIDASE INHIBITOR SCREEN. JRNL REF BIOCHEMISTRY V. 47 10058 2008 JRNL REFN ISSN 0006-2960 JRNL PMID 18759458 JRNL DOI 10.1021/BI8010785 REMARK 2 REMARK 2 RESOLUTION. 1.39 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.146 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.144 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 1.500 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3109 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 203042 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.136 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.135 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.169 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 1.500 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 2723 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 178548 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8193 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 REMARK 3 SOLVENT ATOMS : 1135 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 84747 REMARK 3 NUMBER OF RESTRAINTS : 10428 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 ANGLE DISTANCES (A) : 0.027 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.029 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.062 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.069 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.026 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.046 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.072 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3D4Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAY-08. REMARK 100 THE DEPOSITION ID IS D_1000047598. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-07 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.918 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 207007 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.390 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 7.030 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.39 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.15 REMARK 200 R MERGE FOR SHELL (I) : 0.23500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG8000, TRIS, PH 7, 2.5% MPD, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K, PH 7.00 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 34.32450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 68.88100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 54.65150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 68.88100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.32450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 54.65150 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ARG A 1 REMARK 465 SER A 2 REMARK 465 SER A 3 REMARK 465 HIS A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 HIS A 9 REMARK 465 GLY A 10 REMARK 465 GLU A 11 REMARK 465 PHE A 12 REMARK 465 ASP A 13 REMARK 465 ASP A 14 REMARK 465 PRO A 15 REMARK 465 ILE A 16 REMARK 465 ARG A 17 REMARK 465 PRO A 18 REMARK 465 PRO A 19 REMARK 465 LEU A 20 REMARK 465 LYS A 21 REMARK 465 VAL A 22 REMARK 465 ALA A 23 REMARK 465 ARG A 24 REMARK 465 SER A 25 REMARK 465 PRO A 26 REMARK 465 ARG A 27 REMARK 465 PRO A 28 REMARK 465 GLY A 29 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 GLN A 30 CG CD OE1 NE2 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 HIS A 79 85.64 -163.47 REMARK 500 TRP A 95 -86.19 -173.77 REMARK 500 ASP A 106 -64.00 -130.24 REMARK 500 THR A 162 -66.03 66.08 REMARK 500 GLN A 227 -51.02 -137.75 REMARK 500 ASP A 340 -173.00 -173.00 REMARK 500 LYS A 345 -66.85 -91.57 REMARK 500 SER A 411 -126.87 42.82 REMARK 500 HIS A 470 150.69 -49.62 REMARK 500 ILE A 549 -50.44 -138.43 REMARK 500 LEU A 550 112.65 -162.20 REMARK 500 PRO A 562 40.92 -81.74 REMARK 500 ASN A 732 57.42 -90.59 REMARK 500 SER A 762 -5.65 69.61 REMARK 500 SER A 833 -14.35 -147.83 REMARK 500 ASP A 839 -161.13 -127.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 954 0.30 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL 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 A1046 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 90 NE2 REMARK 620 2 ASP A 92 OD1 92.3 REMARK 620 3 ASP A 204 OD2 98.8 166.2 REMARK 620 4 HIS A 471 NE2 106.6 94.3 90.4 REMARK 620 5 GIM A1048 O3 159.0 85.7 81.0 94.4 REMARK 620 6 GIM A1048 O2 87.7 87.4 84.9 165.6 71.4 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1046 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD A 1047 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GIM A 1048 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HTY RELATED DB: PDB REMARK 900 DGMII + TRIS REMARK 900 RELATED ID: 1HWW RELATED DB: PDB REMARK 900 DGMII + SWAINSONINE REMARK 900 RELATED ID: 1HXK RELATED DB: PDB REMARK 900 DGMII + DEOXYMANNOJIRIMICIN REMARK 900 RELATED ID: 1PS2 RELATED DB: PDB REMARK 900 DGMII + KIFUNENSINE REMARK 900 RELATED ID: 1QWN RELATED DB: PDB REMARK 900 DGMII + 5FLUORO-GULOSYLFLUORIDE REMARK 900 RELATED ID: 1QWU RELATED DB: PDB REMARK 900 DGMII ACID-BASE CATALYST MUTANT D34N1 + 5FLUORO-GULOSYLFLUORIDE REMARK 900 RELATED ID: 1QX1 RELATED DB: PDB REMARK 900 DGMII ACID-BASE CATALYST MUTANT D341N + 2F-MANNOSYLF REMARK 900 RELATED ID: 1R33 RELATED DB: PDB REMARK 900 DGMII + 5-THIO-D-MANNOPYRANOSYLAMINE REMARK 900 RELATED ID: 1R34 RELATED DB: PDB REMARK 900 DGMII + 5-THIO-D-MANNOPYRANOSYLAMIDINIUM SALT REMARK 900 RELATED ID: 2ALW RELATED DB: PDB REMARK 900 DGMII + NOEUROMYCIN REMARK 900 RELATED ID: 2F7O RELATED DB: PDB REMARK 900 DGMII + MANNOSTATIN A REMARK 900 RELATED ID: 2F7P RELATED DB: PDB REMARK 900 DGMII + BENZYL-MANNOSTATIN A REMARK 900 RELATED ID: 2F7Q RELATED DB: PDB REMARK 900 DGMII + AMINOCYCLOPENTITETROL REMARK 900 RELATED ID: 2F7R RELATED DB: PDB REMARK 900 DGMII + BENZYL-AMINOCYCLOPENTITETROL REMARK 900 RELATED ID: 3BUB RELATED DB: PDB REMARK 900 DGMII EMPTY ACTIVE SITE REMARK 900 RELATED ID: 3BUD RELATED DB: PDB REMARK 900 DGMII NUCLEOPHILE MUTANT D204A EMPTY ACTIVE SITE REMARK 900 RELATED ID: 3BUI RELATED DB: PDB REMARK 900 DGMII NUCLEOPHILE MUTANT D204A + TRIS REMARK 900 RELATED ID: 3BUP RELATED DB: PDB REMARK 900 DGMII ACID-BASE CATALYST MUTANT D341N + MANNOSE REMARK 900 RELATED ID: 3BUQ RELATED DB: PDB REMARK 900 DGMII NUCLEOPHILE MUTANT D204A + MANNOSE REMARK 900 RELATED ID: 3BVT RELATED DB: PDB REMARK 900 DGMII NUCLEOPHILE MUTANT D204A + THIO ALPHA1,3 DIMANNOSE REMARK 900 RELATED ID: 3BVU RELATED DB: PDB REMARK 900 DGMII NUCLEOPHILE MUTANT D204A + THIO-ALPHA 1->3, MAN3 REMARK 900 RELATED ID: 3BVV RELATED DB: PDB REMARK 900 DGMII NUCLEOPHILE MUTANT D204A + THIO ALPHA 1->6 MAN4 REMARK 900 RELATED ID: 3BVW RELATED DB: PDB REMARK 900 DGMII NUCLEOPHILE MUTANT D204A + THIO ALPHA 1->6 MAN4-GLCNAC REMARK 900 RELATED ID: 3BVX RELATED DB: PDB REMARK 900 DGMII NUCLEOPHILE MUTANT D204A + MAN4-GLCNAC REMARK 900 RELATED ID: 3CV5 RELATED DB: PDB REMARK 900 DGMII NUCLEOPHILE MUTANT D204A + ALPHA-3 ALPHA-6 MANOPENTAOSE REMARK 900 RELATED ID: 3CZN RELATED DB: PDB REMARK 900 GOLGI ALPHA-MANNOSIDASE II (D204A NUCLEOPHILE MUTANT) IN COMPLEX REMARK 900 WITH GNMAN5GN REMARK 900 RELATED ID: 3CZS RELATED DB: PDB REMARK 900 GOLGI ALPHA-MANNOSIDASE II (D204A NUCLEOPHILE MUTANT) REMARK 900 RELATED ID: 3D4Y RELATED DB: PDB REMARK 900 GOLGI MANNOSIDASE II COMPLEX WITH MANNOIMIDAZOLE REMARK 900 RELATED ID: 3D50 RELATED DB: PDB REMARK 900 GOLGI MANNOSIDASE II COMPLEX WITH N-OCTYL-6-EPI-VALIENAMINE REMARK 900 RELATED ID: 3D51 RELATED DB: PDB REMARK 900 GOLGI MANNOSIDASE II COMPLEX WITH GLUCO-HYDROXYIMINOLACTAM REMARK 900 RELATED ID: 3D52 RELATED DB: PDB REMARK 900 GOLGI MANNOSIDASE II COMPLEX WITH AN N-ARYL CARBAMATE DERIVATIVE OF REMARK 900 GLUCO-HYDROXYIMINOLACTAM REMARK 999 REMARK 999 SEQUENCE REMARK 999 E970K CONFLICT IN UNP ENTRY Q24451 DBREF 3D4Z A 13 1045 UNP Q24451 MAN2_DROME 76 1108 SEQADV 3D4Z ARG A 1 UNP Q24451 EXPRESSION TAG SEQADV 3D4Z SER A 2 UNP Q24451 EXPRESSION TAG SEQADV 3D4Z SER A 3 UNP Q24451 EXPRESSION TAG SEQADV 3D4Z HIS A 4 UNP Q24451 EXPRESSION TAG SEQADV 3D4Z HIS A 5 UNP Q24451 EXPRESSION TAG SEQADV 3D4Z HIS A 6 UNP Q24451 EXPRESSION TAG SEQADV 3D4Z HIS A 7 UNP Q24451 EXPRESSION TAG SEQADV 3D4Z HIS A 8 UNP Q24451 EXPRESSION TAG SEQADV 3D4Z HIS A 9 UNP Q24451 EXPRESSION TAG SEQADV 3D4Z GLY A 10 UNP Q24451 EXPRESSION TAG SEQADV 3D4Z GLU A 11 UNP Q24451 EXPRESSION TAG SEQADV 3D4Z PHE A 12 UNP Q24451 EXPRESSION TAG SEQADV 3D4Z LYS A 907 UNP Q24451 GLU 970 SEE REMARK 999 SEQRES 1 A 1045 ARG SER SER HIS HIS HIS HIS HIS HIS GLY GLU PHE ASP SEQRES 2 A 1045 ASP PRO ILE ARG PRO PRO LEU LYS VAL ALA ARG SER PRO SEQRES 3 A 1045 ARG PRO GLY GLN CYS GLN ASP VAL VAL GLN ASP VAL PRO SEQRES 4 A 1045 ASN VAL ASP VAL GLN MET LEU GLU LEU TYR ASP ARG MET SEQRES 5 A 1045 SER PHE LYS ASP ILE ASP GLY GLY VAL TRP LYS GLN GLY SEQRES 6 A 1045 TRP ASN ILE LYS TYR ASP PRO LEU LYS TYR ASN ALA HIS SEQRES 7 A 1045 HIS LYS LEU LYS VAL PHE VAL VAL PRO HIS SER HIS ASN SEQRES 8 A 1045 ASP PRO GLY TRP ILE GLN THR PHE GLU GLU TYR TYR GLN SEQRES 9 A 1045 HIS ASP THR LYS HIS ILE LEU SER ASN ALA LEU ARG HIS SEQRES 10 A 1045 LEU HIS ASP ASN PRO GLU MET LYS PHE ILE TRP ALA GLU SEQRES 11 A 1045 ILE SER TYR PHE ALA ARG PHE TYR HIS ASP LEU GLY GLU SEQRES 12 A 1045 ASN LYS LYS LEU GLN MET LYS SER ILE VAL LYS ASN GLY SEQRES 13 A 1045 GLN LEU GLU PHE VAL THR GLY GLY TRP VAL MET PRO ASP SEQRES 14 A 1045 GLU ALA ASN SER HIS TRP ARG ASN VAL LEU LEU GLN LEU SEQRES 15 A 1045 THR GLU GLY GLN THR TRP LEU LYS GLN PHE MET ASN VAL SEQRES 16 A 1045 THR PRO THR ALA SER TRP ALA ILE ASP PRO PHE GLY HIS SEQRES 17 A 1045 SER PRO THR MET PRO TYR ILE LEU GLN LYS SER GLY PHE SEQRES 18 A 1045 LYS ASN MET LEU ILE GLN ARG THR HIS TYR SER VAL LYS SEQRES 19 A 1045 LYS GLU LEU ALA GLN GLN ARG GLN LEU GLU PHE LEU TRP SEQRES 20 A 1045 ARG GLN ILE TRP ASP ASN LYS GLY ASP THR ALA LEU PHE SEQRES 21 A 1045 THR HIS MET MET PRO PHE TYR SER TYR ASP ILE PRO HIS SEQRES 22 A 1045 THR CYS GLY PRO ASP PRO LYS VAL CYS CYS GLN PHE ASP SEQRES 23 A 1045 PHE LYS ARG MET GLY SER PHE GLY LEU SER CYS PRO TRP SEQRES 24 A 1045 LYS VAL PRO PRO ARG THR ILE SER ASP GLN ASN VAL ALA SEQRES 25 A 1045 ALA ARG SER ASP LEU LEU VAL ASP GLN TRP LYS LYS LYS SEQRES 26 A 1045 ALA GLU LEU TYR ARG THR ASN VAL LEU LEU ILE PRO LEU SEQRES 27 A 1045 GLY ASP ASP PHE ARG PHE LYS GLN ASN THR GLU TRP ASP SEQRES 28 A 1045 VAL GLN ARG VAL ASN TYR GLU ARG LEU PHE GLU HIS ILE SEQRES 29 A 1045 ASN SER GLN ALA HIS PHE ASN VAL GLN ALA GLN PHE GLY SEQRES 30 A 1045 THR LEU GLN GLU TYR PHE ASP ALA VAL HIS GLN ALA GLU SEQRES 31 A 1045 ARG ALA GLY GLN ALA GLU PHE PRO THR LEU SER GLY ASP SEQRES 32 A 1045 PHE PHE THR TYR ALA ASP ARG SER ASP ASN TYR TRP SER SEQRES 33 A 1045 GLY TYR TYR THR SER ARG PRO TYR HIS LYS ARG MET ASP SEQRES 34 A 1045 ARG VAL LEU MET HIS TYR VAL ARG ALA ALA GLU MET LEU SEQRES 35 A 1045 SER ALA TRP HIS SER TRP ASP GLY MET ALA ARG ILE GLU SEQRES 36 A 1045 GLU ARG LEU GLU GLN ALA ARG ARG GLU LEU SER LEU PHE SEQRES 37 A 1045 GLN HIS HIS ASP GLY ILE THR GLY THR ALA LYS THR HIS SEQRES 38 A 1045 VAL VAL VAL ASP TYR GLU GLN ARG MET GLN GLU ALA LEU SEQRES 39 A 1045 LYS ALA CYS GLN MET VAL MET GLN GLN SER VAL TYR ARG SEQRES 40 A 1045 LEU LEU THR LYS PRO SER ILE TYR SER PRO ASP PHE SER SEQRES 41 A 1045 PHE SER TYR PHE THR LEU ASP ASP SER ARG TRP PRO GLY SEQRES 42 A 1045 SER GLY VAL GLU ASP SER ARG THR THR ILE ILE LEU GLY SEQRES 43 A 1045 GLU ASP ILE LEU PRO SER LYS HIS VAL VAL MET HIS ASN SEQRES 44 A 1045 THR LEU PRO HIS TRP ARG GLU GLN LEU VAL ASP PHE TYR SEQRES 45 A 1045 VAL SER SER PRO PHE VAL SER VAL THR ASP LEU ALA ASN SEQRES 46 A 1045 ASN PRO VAL GLU ALA GLN VAL SER PRO VAL TRP SER TRP SEQRES 47 A 1045 HIS HIS ASP THR LEU THR LYS THR ILE HIS PRO GLN GLY SEQRES 48 A 1045 SER THR THR LYS TYR ARG ILE ILE PHE LYS ALA ARG VAL SEQRES 49 A 1045 PRO PRO MET GLY LEU ALA THR TYR VAL LEU THR ILE SER SEQRES 50 A 1045 ASP SER LYS PRO GLU HIS THR SER TYR ALA SER ASN LEU SEQRES 51 A 1045 LEU LEU ARG LYS ASN PRO THR SER LEU PRO LEU GLY GLN SEQRES 52 A 1045 TYR PRO GLU ASP VAL LYS PHE GLY ASP PRO ARG GLU ILE SEQRES 53 A 1045 SER LEU ARG VAL GLY ASN GLY PRO THR LEU ALA PHE SER SEQRES 54 A 1045 GLU GLN GLY LEU LEU LYS SER ILE GLN LEU THR GLN ASP SEQRES 55 A 1045 SER PRO HIS VAL PRO VAL HIS PHE LYS PHE LEU LYS TYR SEQRES 56 A 1045 GLY VAL ARG SER HIS GLY ASP ARG SER GLY ALA TYR LEU SEQRES 57 A 1045 PHE LEU PRO ASN GLY PRO ALA SER PRO VAL GLU LEU GLY SEQRES 58 A 1045 GLN PRO VAL VAL LEU VAL THR LYS GLY LYS LEU GLU SER SEQRES 59 A 1045 SER VAL SER VAL GLY LEU PRO SER VAL VAL HIS GLN THR SEQRES 60 A 1045 ILE MET ARG GLY GLY ALA PRO GLU ILE ARG ASN LEU VAL SEQRES 61 A 1045 ASP ILE GLY SER LEU ASP ASN THR GLU ILE VAL MET ARG SEQRES 62 A 1045 LEU GLU THR HIS ILE ASP SER GLY ASP ILE PHE TYR THR SEQRES 63 A 1045 ASP LEU ASN GLY LEU GLN PHE ILE LYS ARG ARG ARG LEU SEQRES 64 A 1045 ASP LYS LEU PRO LEU GLN ALA ASN TYR TYR PRO ILE PRO SEQRES 65 A 1045 SER GLY MET PHE ILE GLU ASP ALA ASN THR ARG LEU THR SEQRES 66 A 1045 LEU LEU THR GLY GLN PRO LEU GLY GLY SER SER LEU ALA SEQRES 67 A 1045 SER GLY GLU LEU GLU ILE MET GLN ASP ARG ARG LEU ALA SEQRES 68 A 1045 SER ASP ASP GLU ARG GLY LEU GLY GLN GLY VAL LEU ASP SEQRES 69 A 1045 ASN LYS PRO VAL LEU HIS ILE TYR ARG LEU VAL LEU GLU SEQRES 70 A 1045 LYS VAL ASN ASN CYS VAL ARG PRO SER LYS LEU HIS PRO SEQRES 71 A 1045 ALA GLY TYR LEU THR SER ALA ALA HIS LYS ALA SER GLN SEQRES 72 A 1045 SER LEU LEU ASP PRO LEU ASP LYS PHE ILE PHE ALA GLU SEQRES 73 A 1045 ASN GLU TRP ILE GLY ALA GLN GLY GLN PHE GLY GLY ASP SEQRES 74 A 1045 HIS PRO SER ALA ARG GLU ASP LEU ASP VAL SER VAL MET SEQRES 75 A 1045 ARG ARG LEU THR LYS SER SER ALA LYS THR GLN ARG VAL SEQRES 76 A 1045 GLY TYR VAL LEU HIS ARG THR ASN LEU MET GLN CYS GLY SEQRES 77 A 1045 THR PRO GLU GLU HIS THR GLN LYS LEU ASP VAL CYS HIS SEQRES 78 A 1045 LEU LEU PRO ASN VAL ALA ARG CYS GLU ARG THR THR LEU SEQRES 79 A 1045 THR PHE LEU GLN ASN LEU GLU HIS LEU ASP GLY MET VAL SEQRES 80 A 1045 ALA PRO GLU VAL CYS PRO MET GLU THR ALA ALA TYR VAL SEQRES 81 A 1045 SER SER HIS SER SER HET ZN A1046 1 HET MRD A1047 8 HET GIM A1048 14 HETNAM ZN ZINC ION HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL HETNAM GIM GLUCOIMIDAZOLE HETSYN GIM (5S,6S,7R,8R)-5-(HYDROXYMETHYL)-1,5,6,7,8,8A- HETSYN 2 GIM HEXAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL FORMUL 2 ZN ZN 2+ FORMUL 3 MRD C6 H14 O2 FORMUL 4 GIM C8 H13 N2 O4 1+ FORMUL 5 HOH *1135(H2 O) HELIX 1 1 MET A 45 MET A 52 1 8 HELIX 2 2 ASP A 71 TYR A 75 5 5 HELIX 3 3 THR A 98 ASP A 106 1 9 HELIX 4 4 ASP A 106 ASN A 121 1 16 HELIX 5 5 GLU A 130 HIS A 139 1 10 HELIX 6 6 GLY A 142 ASN A 155 1 14 HELIX 7 7 HIS A 174 ASN A 194 1 21 HELIX 8 8 PRO A 210 LYS A 218 1 9 HELIX 9 9 HIS A 230 GLN A 240 1 11 HELIX 10 10 ASP A 270 THR A 274 5 5 HELIX 11 11 ASP A 278 CYS A 283 1 6 HELIX 12 12 GLN A 284 MET A 290 5 7 HELIX 13 13 ASN A 310 GLU A 327 1 18 HELIX 14 14 GLN A 346 GLN A 367 1 22 HELIX 15 15 ALA A 368 PHE A 370 5 3 HELIX 16 16 THR A 378 ALA A 392 1 15 HELIX 17 17 SER A 416 THR A 420 5 5 HELIX 18 18 ARG A 422 TRP A 445 1 24 HELIX 19 19 ASP A 449 ALA A 452 5 4 HELIX 20 20 ARG A 453 GLN A 469 1 17 HELIX 21 21 LYS A 479 LEU A 509 1 31 HELIX 22 22 PRO A 823 TYR A 828 5 6 HELIX 23 23 THR A 915 ASP A 927 1 13 HELIX 24 24 ASP A 998 LEU A 1002 5 5 HELIX 25 25 ASP A 1024 VAL A 1027 5 4 SHEET 1 A 6 VAL A 43 GLN A 44 0 SHEET 2 A 6 THR A 399 SER A 401 1 O SER A 401 N VAL A 43 SHEET 3 A 6 GLU A 244 TRP A 247 1 N LEU A 246 O LEU A 400 SHEET 4 A 6 LEU A 259 MET A 263 -1 O THR A 261 N PHE A 245 SHEET 5 A 6 ASN A 223 ILE A 226 1 N MET A 224 O HIS A 262 SHEET 6 A 6 ALA A 199 ALA A 202 1 N ALA A 202 O LEU A 225 SHEET 1 B 3 VAL A 333 ASP A 341 0 SHEET 2 B 3 LEU A 81 HIS A 90 1 N LYS A 82 O LEU A 334 SHEET 3 B 3 VAL A 372 PHE A 376 1 O GLN A 375 N VAL A 85 SHEET 1 C 2 PHE A 126 TRP A 128 0 SHEET 2 C 2 LEU A 158 PHE A 160 1 O GLU A 159 N PHE A 126 SHEET 1 D 2 ALA A 408 ARG A 410 0 SHEET 2 D 2 ASN A 413 TYR A 414 -1 O ASN A 413 N ARG A 410 SHEET 1 E 6 PHE A 524 ASP A 527 0 SHEET 2 E 6 ASP A 930 PHE A 934 -1 O ILE A 933 N THR A 525 SHEET 3 E 6 SER A 552 ASN A 559 -1 N VAL A 556 O PHE A 932 SHEET 4 E 6 GLY A 628 ILE A 636 -1 O TYR A 632 N VAL A 555 SHEET 5 E 6 VAL A 578 ASP A 582 -1 N THR A 581 O VAL A 633 SHEET 6 E 6 PRO A 587 VAL A 588 -1 O VAL A 588 N VAL A 580 SHEET 1 F 5 PHE A 524 ASP A 527 0 SHEET 2 F 5 ASP A 930 PHE A 934 -1 O ILE A 933 N THR A 525 SHEET 3 F 5 SER A 552 ASN A 559 -1 N VAL A 556 O PHE A 932 SHEET 4 F 5 GLY A 628 ILE A 636 -1 O TYR A 632 N VAL A 555 SHEET 5 F 5 GLN A 945 PHE A 946 -1 O PHE A 946 N LEU A 629 SHEET 1 G 5 THR A 542 ILE A 543 0 SHEET 2 G 5 ARG A 565 VAL A 573 1 O TYR A 572 N ILE A 543 SHEET 3 G 5 THR A 606 VAL A 624 -1 O ILE A 618 N PHE A 571 SHEET 4 G 5 ALA A 590 ASP A 601 -1 N SER A 597 O GLN A 610 SHEET 5 G 5 THR A 644 TYR A 646 1 O SER A 645 N VAL A 592 SHEET 1 H12 LYS A 669 GLY A 671 0 SHEET 2 H12 SER A 648 LEU A 652 1 N LEU A 651 O LYS A 669 SHEET 3 H12 VAL A 745 LYS A 749 -1 O VAL A 745 N LEU A 652 SHEET 4 H12 SER A 754 LEU A 760 -1 O SER A 757 N LEU A 746 SHEET 5 H12 VAL A 763 MET A 769 -1 O MET A 769 N SER A 754 SHEET 6 H12 GLU A 775 VAL A 780 -1 O GLU A 775 N ILE A 768 SHEET 7 H12 VAL A 888 LYS A 898 -1 O VAL A 888 N VAL A 780 SHEET 8 H12 THR A 842 THR A 848 -1 N THR A 845 O VAL A 895 SHEET 9 H12 GLY A 834 GLU A 838 -1 N MET A 835 O LEU A 846 SHEET 10 H12 ILE A 803 LEU A 808 -1 N TYR A 805 O PHE A 836 SHEET 11 H12 GLN A 812 ARG A 817 -1 O ARG A 816 N PHE A 804 SHEET 12 H12 ALA A 911 GLY A 912 -1 O GLY A 912 N PHE A 813 SHEET 1 I 5 ILE A 676 ARG A 679 0 SHEET 2 I 5 THR A 685 PHE A 688 -1 O PHE A 688 N ILE A 676 SHEET 3 I 5 LEU A 694 GLN A 698 -1 O LYS A 695 N ALA A 687 SHEET 4 I 5 HIS A 705 TYR A 715 -1 O VAL A 706 N ILE A 697 SHEET 5 I 5 SER A 736 PRO A 737 -1 O SER A 736 N LYS A 714 SHEET 1 J 8 ILE A 676 ARG A 679 0 SHEET 2 J 8 THR A 685 PHE A 688 -1 O PHE A 688 N ILE A 676 SHEET 3 J 8 LEU A 694 GLN A 698 -1 O LYS A 695 N ALA A 687 SHEET 4 J 8 HIS A 705 TYR A 715 -1 O VAL A 706 N ILE A 697 SHEET 5 J 8 THR A 788 THR A 796 -1 O ARG A 793 N LYS A 711 SHEET 6 J 8 GLU A 861 ARG A 869 -1 O GLN A 866 N ILE A 790 SHEET 7 J 8 LEU A 852 SER A 855 -1 N GLY A 853 O MET A 865 SHEET 8 J 8 TYR A 829 ILE A 831 -1 N TYR A 829 O GLY A 854 SHEET 1 K 5 LEU A 957 ARG A 964 0 SHEET 2 K 5 THR A 972 ARG A 981 -1 O GLY A 976 N ARG A 963 SHEET 3 K 5 THR A1036 SER A1044 -1 O ALA A1037 N LEU A 979 SHEET 4 K 5 VAL A1006 THR A1012 -1 N ALA A1007 O SER A1042 SHEET 5 K 5 ASN A1019 HIS A1022 -1 O LEU A1020 N ARG A1011 SSBOND 1 CYS A 31 CYS A 1032 1555 1555 2.09 SSBOND 2 CYS A 275 CYS A 282 1555 1555 2.03 SSBOND 3 CYS A 283 CYS A 297 1555 1555 2.09 SSBOND 4 CYS A 902 CYS A 987 1555 1555 2.06 SSBOND 5 CYS A 1000 CYS A 1009 1555 1555 2.00 LINK NE2 HIS A 90 ZN ZN A1046 1555 1555 2.03 LINK OD1 ASP A 92 ZN ZN A1046 1555 1555 2.10 LINK OD2 ASP A 204 ZN ZN A1046 1555 1555 2.06 LINK NE2 HIS A 471 ZN ZN A1046 1555 1555 2.09 LINK ZN ZN A1046 O3 GIM A1048 1555 1555 2.26 LINK ZN ZN A1046 O2 GIM A1048 1555 1555 2.39 CISPEP 1 PHE A 405 THR A 406 0 -5.32 CISPEP 2 TRP A 531 PRO A 532 0 -8.06 SITE 1 AC1 4 HIS A 90 ASP A 92 ASP A 204 HIS A 471 SITE 1 AC2 8 LYS A 63 GLN A 64 TYR A 267 HIS A 273 SITE 2 AC2 8 HOH A1652 HOH A1654 HOH A1655 HOH A1698 SITE 1 AC3 14 HIS A 90 ASP A 92 TRP A 95 ASP A 204 SITE 2 AC3 14 PHE A 206 ARG A 228 TYR A 269 ASP A 341 SITE 3 AC3 14 TRP A 415 HIS A 471 ASP A 472 TYR A 727 SITE 4 AC3 14 ARG A 876 HOH A1710 CRYST1 68.649 109.303 137.762 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.014567 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009149 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007259 0.00000