HEADER TRANSFERASE 10-MAY-11 2YI1 TITLE CRYSTAL STRUCTURE OF N-ACETYLMANNOSAMINE KINASE IN COMPLEX WITH N- TITLE 2 ACETYL MANNOSAMINE 6-PHOSPHATE AND ADP. COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIFUNCTIONAL UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE/N- COMPND 3 ACETYLMANNOSAMINE KINASE; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: N-ACETYLMANNOSAMINE KINASE DOMAIN, RESIDUES 406-720; COMPND 6 SYNONYM: N-ACETYL MANNOSAMINE KINASE, MANAC KINASE, UDP-GLCNAC-2- COMPND 7 EPIMERASE/MANAC KINASE; COMPND 8 EC: 2.7.1.60; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-RIL; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET28A; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A-MNK KEYWDS TRANSFERASE, SUGAR KINASE, ROK FAMILY EXPDTA X-RAY DIFFRACTION AUTHOR J.MARTINEZ,L.D.NGUYEN,E.TAUBERGER,S.HINDERLICH,W.REUTTER,H.FAN, AUTHOR 2 W.SAENGER,S.MONIOT REVDAT 5 20-DEC-23 2YI1 1 HETSYN REVDAT 4 29-JUL-20 2YI1 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE REVDAT 3 02-MAY-12 2YI1 1 JRNL REVDAT 2 14-MAR-12 2YI1 1 LINK REVDAT 1 29-FEB-12 2YI1 0 JRNL AUTH J.MARTINEZ,L.D.NGUYEN,E.TAUBERGER,S.HINDERLICH,W.REUTTER, JRNL AUTH 2 H.FAN,W.SAENGER,S.MONIOT JRNL TITL CRYSTAL STRUCTURES OF N-ACETYLMANNOSAMINE KINASE PROVIDE JRNL TITL 2 INSIGHTS INTO ENZYME SPECIFICITY AND INHIBITION JRNL REF J.BIOL.CHEM. V. 287 13656 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22343627 JRNL DOI 10.1074/JBC.M111.318170 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 22395 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1179 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) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1630 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.1770 REMARK 3 BIN FREE R VALUE SET COUNT : 86 REMARK 3 BIN FREE R VALUE : 0.2180 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2270 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 117 REMARK 3 SOLVENT ATOMS : 143 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.37000 REMARK 3 B22 (A**2) : 0.37000 REMARK 3 B33 (A**2) : -0.74000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.171 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.143 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.089 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.828 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2517 ; 0.022 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1626 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3416 ; 1.788 ; 2.003 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4028 ; 1.014 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 329 ; 6.465 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 90 ;36.285 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 414 ;15.252 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;24.751 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 410 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2779 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 447 ; 0.002 ; 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): 1587 ; 0.976 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 664 ; 0.289 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2549 ; 1.756 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 930 ; 3.007 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 867 ; 4.808 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 405 A 597 REMARK 3 ORIGIN FOR THE GROUP (A): 28.8130 1.1340 -7.1260 REMARK 3 T TENSOR REMARK 3 T11: 0.0597 T22: 0.0764 REMARK 3 T33: 0.0841 T12: 0.0058 REMARK 3 T13: 0.0043 T23: 0.0054 REMARK 3 L TENSOR REMARK 3 L11: 0.4857 L22: 1.5158 REMARK 3 L33: 1.3035 L12: -0.2661 REMARK 3 L13: 0.0049 L23: -0.3321 REMARK 3 S TENSOR REMARK 3 S11: 0.0330 S12: 0.0048 S13: -0.0713 REMARK 3 S21: -0.1396 S22: 0.0105 S23: -0.0167 REMARK 3 S31: 0.1968 S32: 0.0628 S33: -0.0435 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 598 A 642 REMARK 3 ORIGIN FOR THE GROUP (A): 50.1670 18.3890 4.7390 REMARK 3 T TENSOR REMARK 3 T11: 0.1286 T22: 1.1530 REMARK 3 T33: 0.4988 T12: -0.0237 REMARK 3 T13: -0.0744 T23: 0.1071 REMARK 3 L TENSOR REMARK 3 L11: 46.0680 L22: 3.5960 REMARK 3 L33: 20.8076 L12: -5.3588 REMARK 3 L13: 4.8705 L23: 2.3053 REMARK 3 S TENSOR REMARK 3 S11: -0.7437 S12: -0.5898 S13: 1.0659 REMARK 3 S21: 0.2674 S22: 0.0437 S23: -0.7381 REMARK 3 S31: -0.0829 S32: 3.1493 S33: 0.6999 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 643 A 717 REMARK 3 ORIGIN FOR THE GROUP (A): 26.7640 11.8790 8.0340 REMARK 3 T TENSOR REMARK 3 T11: 0.0524 T22: 0.0898 REMARK 3 T33: 0.0554 T12: 0.0154 REMARK 3 T13: -0.0202 T23: 0.0165 REMARK 3 L TENSOR REMARK 3 L11: 0.6696 L22: 2.4862 REMARK 3 L33: 1.7306 L12: -0.4012 REMARK 3 L13: -0.2564 L23: 1.0261 REMARK 3 S TENSOR REMARK 3 S11: -0.0887 S12: -0.1682 S13: -0.0276 REMARK 3 S21: 0.2642 S22: 0.1249 S23: -0.0559 REMARK 3 S31: 0.1106 S32: 0.1836 S33: -0.0362 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 2YI1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-MAY-11. REMARK 100 THE DEPOSITION ID IS D_1290048251. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL 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 : BESSY REMARK 200 BEAMLINE : 14.2 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 : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24925 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 41.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.1000 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) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.69000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 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: PDB ENTRY 2YHW REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M CALCIUM ACETATE, 0.1M SODIUM REMARK 280 CACODYLATE PH 6.5 AND 40% PEG 300 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 50.74500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 45.35000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 45.35000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.37250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 45.35000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 45.35000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 76.11750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 45.35000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.35000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 25.37250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 45.35000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.35000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 76.11750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 50.74500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -59.9 KCAL/MOL 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 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 MET A 378 REMARK 465 GLY A 379 REMARK 465 SER A 380 REMARK 465 SER A 381 REMARK 465 HIS A 382 REMARK 465 HIS A 383 REMARK 465 HIS A 384 REMARK 465 HIS A 385 REMARK 465 HIS A 386 REMARK 465 HIS A 387 REMARK 465 SER A 388 REMARK 465 SER A 389 REMARK 465 GLY A 390 REMARK 465 LEU A 391 REMARK 465 VAL A 392 REMARK 465 PRO A 393 REMARK 465 ARG A 394 REMARK 465 GLY A 395 REMARK 465 SER A 396 REMARK 465 HIS A 397 REMARK 465 MET A 398 REMARK 465 GLU A 399 REMARK 465 ASN A 400 REMARK 465 LEU A 401 REMARK 465 TYR A 402 REMARK 465 PHE A 403 REMARK 465 GLN A 404 REMARK 465 VAL A 616 REMARK 465 PRO A 617 REMARK 465 LYS A 618 REMARK 465 ASP A 619 REMARK 465 GLU A 620 REMARK 465 THR A 718 REMARK 465 ARG A 719 REMARK 465 ARG A 720 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 GLU A 606 CG CD OE1 OE2 REMARK 470 GLU A 612 CG CD OE1 OE2 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 THR A 406 117.15 -32.58 REMARK 500 TRP A 495 66.49 -150.63 REMARK 500 HIS A 554 -2.07 74.06 REMARK 500 ASP A 575 -104.89 -122.10 REMARK 500 GLU A 606 24.11 -75.84 REMARK 500 THR A 659 -65.79 -92.64 REMARK 500 ASP A 703 82.73 -151.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 2-(ACETYLAMINO)-6-(PHOSPHATE)-2-DEOXY-ALPHA-D-MANNOPYRANOSE REMARK 600 (BMX): N ACETYL MANNOSAMINE PHOSPHORYLATED AT THE C6 REMARK 600 POSITION. REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 2PE A 1720 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 MG A1717 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 413 OD2 REMARK 620 2 ADP A1727 O1B 146.8 REMARK 620 3 HOH A2002 O 80.7 87.9 REMARK 620 4 HOH A2004 O 63.4 88.9 101.6 REMARK 620 5 HOH A2142 O 113.1 96.7 85.3 171.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1719 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 516 OD1 REMARK 620 2 GLY A 548 O 96.8 REMARK 620 3 ALA A 565 O 157.4 78.4 REMARK 620 4 HOH A2066 O 80.6 92.2 77.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1719 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 564 O REMARK 620 2 HOH A2046 O 110.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A2000 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 569 ND1 REMARK 620 2 CYS A 579 SG 102.3 REMARK 620 3 CYS A 581 SG 105.7 104.2 REMARK 620 4 CYS A 586 SG 121.8 109.8 111.3 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2YHY RELATED DB: PDB REMARK 900 STRUCTURE OF N-ACETYLMANNOSAMINE KINASE IN COMPLEX WITH N- REMARK 900 ACETYLMANNOSAMINE AND ADP REMARK 900 RELATED ID: 2YHW RELATED DB: PDB REMARK 900 HIGH-RESOLUTION CRYSTAL STRUCTURES OF N-ACETYLMANNOSAMINE KINASE: REMARK 900 INSIGHTS ABOUT SUBSTRATE SPECIFICITY, ACTIVITY AND INHIBITOR REMARK 900 MODELLING. DBREF 2YI1 A 406 720 UNP Q9Y223 GLCNE_HUMAN 406 720 SEQADV 2YI1 MET A 378 UNP Q9Y223 EXPRESSION TAG SEQADV 2YI1 GLY A 379 UNP Q9Y223 EXPRESSION TAG SEQADV 2YI1 SER A 380 UNP Q9Y223 EXPRESSION TAG SEQADV 2YI1 SER A 381 UNP Q9Y223 EXPRESSION TAG SEQADV 2YI1 HIS A 382 UNP Q9Y223 EXPRESSION TAG SEQADV 2YI1 HIS A 383 UNP Q9Y223 EXPRESSION TAG SEQADV 2YI1 HIS A 384 UNP Q9Y223 EXPRESSION TAG SEQADV 2YI1 HIS A 385 UNP Q9Y223 EXPRESSION TAG SEQADV 2YI1 HIS A 386 UNP Q9Y223 EXPRESSION TAG SEQADV 2YI1 HIS A 387 UNP Q9Y223 EXPRESSION TAG SEQADV 2YI1 SER A 388 UNP Q9Y223 EXPRESSION TAG SEQADV 2YI1 SER A 389 UNP Q9Y223 EXPRESSION TAG SEQADV 2YI1 GLY A 390 UNP Q9Y223 EXPRESSION TAG SEQADV 2YI1 LEU A 391 UNP Q9Y223 EXPRESSION TAG SEQADV 2YI1 VAL A 392 UNP Q9Y223 EXPRESSION TAG SEQADV 2YI1 PRO A 393 UNP Q9Y223 EXPRESSION TAG SEQADV 2YI1 ARG A 394 UNP Q9Y223 EXPRESSION TAG SEQADV 2YI1 GLY A 395 UNP Q9Y223 EXPRESSION TAG SEQADV 2YI1 SER A 396 UNP Q9Y223 EXPRESSION TAG SEQADV 2YI1 HIS A 397 UNP Q9Y223 EXPRESSION TAG SEQADV 2YI1 MET A 398 UNP Q9Y223 EXPRESSION TAG SEQADV 2YI1 GLU A 399 UNP Q9Y223 EXPRESSION TAG SEQADV 2YI1 ASN A 400 UNP Q9Y223 EXPRESSION TAG SEQADV 2YI1 LEU A 401 UNP Q9Y223 EXPRESSION TAG SEQADV 2YI1 TYR A 402 UNP Q9Y223 EXPRESSION TAG SEQADV 2YI1 PHE A 403 UNP Q9Y223 EXPRESSION TAG SEQADV 2YI1 GLN A 404 UNP Q9Y223 EXPRESSION TAG SEQADV 2YI1 GLY A 405 UNP Q9Y223 EXPRESSION TAG SEQRES 1 A 343 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 343 LEU VAL PRO ARG GLY SER HIS MET GLU ASN LEU TYR PHE SEQRES 3 A 343 GLN GLY THR LEU SER ALA LEU ALA VAL ASP LEU GLY GLY SEQRES 4 A 343 THR ASN LEU ARG VAL ALA ILE VAL SER MET LYS GLY GLU SEQRES 5 A 343 ILE VAL LYS LYS TYR THR GLN PHE ASN PRO LYS THR TYR SEQRES 6 A 343 GLU GLU ARG ILE ASN LEU ILE LEU GLN MET CYS VAL GLU SEQRES 7 A 343 ALA ALA ALA GLU ALA VAL LYS LEU ASN CYS ARG ILE LEU SEQRES 8 A 343 GLY VAL GLY ILE SER THR GLY GLY ARG VAL ASN PRO ARG SEQRES 9 A 343 GLU GLY ILE VAL LEU HIS SER THR LYS LEU ILE GLN GLU SEQRES 10 A 343 TRP ASN SER VAL ASP LEU ARG THR PRO LEU SER ASP THR SEQRES 11 A 343 LEU HIS LEU PRO VAL TRP VAL ASP ASN ASP GLY ASN CYS SEQRES 12 A 343 ALA ALA LEU ALA GLU ARG LYS PHE GLY GLN GLY LYS GLY SEQRES 13 A 343 LEU GLU ASN PHE VAL THR LEU ILE THR GLY THR GLY ILE SEQRES 14 A 343 GLY GLY GLY ILE ILE HIS GLN HIS GLU LEU ILE HIS GLY SEQRES 15 A 343 SER SER PHE CYS ALA ALA GLU LEU GLY HIS LEU VAL VAL SEQRES 16 A 343 SER LEU ASP GLY PRO ASP CYS SER CYS GLY SER HIS GLY SEQRES 17 A 343 CYS ILE GLU ALA TYR ALA SER GLY MET ALA LEU GLN ARG SEQRES 18 A 343 GLU ALA LYS LYS LEU HIS ASP GLU ASP LEU LEU LEU VAL SEQRES 19 A 343 GLU GLY MET SER VAL PRO LYS ASP GLU ALA VAL GLY ALA SEQRES 20 A 343 LEU HIS LEU ILE GLN ALA ALA LYS LEU GLY ASN ALA LYS SEQRES 21 A 343 ALA GLN SER ILE LEU ARG THR ALA GLY THR ALA LEU GLY SEQRES 22 A 343 LEU GLY VAL VAL ASN ILE LEU HIS THR MET ASN PRO SER SEQRES 23 A 343 LEU VAL ILE LEU SER GLY VAL LEU ALA SER HIS TYR ILE SEQRES 24 A 343 HIS ILE VAL LYS ASP VAL ILE ARG GLN GLN ALA LEU SER SEQRES 25 A 343 SER VAL GLN ASP VAL ASP VAL VAL VAL SER ASP LEU VAL SEQRES 26 A 343 ASP PRO ALA LEU LEU GLY ALA ALA SER MET VAL LEU ASP SEQRES 27 A 343 TYR THR THR ARG ARG HET BMX A1000 19 HET BM3 A1001 15 HET MG A1717 1 HET CA A1718 1 HET CA A1719 2 HET 2PE A1720 19 HET PG4 A1721 13 HET EDO A1722 4 HET EDO A1723 4 HET EDO A1724 4 HET EDO A1725 4 HET ACT A1726 4 HET ADP A1727 27 HET ZN A2000 1 HETNAM BMX 2-ACETAMIDO-2-DEOXY-6-O-PHOSPHONO-ALPHA-D-MANNOPYRANOSE HETNAM BM3 2-ACETAMIDO-2-DEOXY-ALPHA-D-MANNOPYRANOSE HETNAM MG MAGNESIUM ION HETNAM CA CALCIUM ION HETNAM 2PE NONAETHYLENE GLYCOL HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM EDO 1,2-ETHANEDIOL HETNAM ACT ACETATE ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM ZN ZINC ION HETSYN BMX 2-(ACETYLAMINO)-2-DEOXY-6-O-PHOSPHONO-ALPHA-D- HETSYN 2 BMX MANNOPYRANOSE; N-ACETYL-6-O-PHOSPHONO-ALPHA-D- HETSYN 3 BMX MANNOSAMINE; 2-ACETAMIDO-2-DEOXY-6-O-PHOSPHONO-ALPHA- HETSYN 4 BMX D-MANNOSE; 2-ACETAMIDO-2-DEOXY-6-O-PHOSPHONO-D- HETSYN 5 BMX MANNOSE; 2-ACETAMIDO-2-DEOXY-6-O-PHOSPHONO-MANNOSE HETSYN BM3 N-ACETYL-ALPHA-D-MANNOSAMINE; 2-ACETAMIDO-2-DEOXY- HETSYN 2 BM3 ALPHA-D-MANNOSE; 2-ACETAMIDO-2-DEOXY-D-MANNOSE; 2- HETSYN 3 BM3 ACETAMIDO-2-DEOXY-MANNOSE; 2-(ACETYLAMINO)-2-DEOXY- HETSYN 4 BM3 ALPHA-D-MANNOPYRANOSE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 BMX C8 H16 N O9 P FORMUL 3 BM3 C8 H15 N O6 FORMUL 4 MG MG 2+ FORMUL 5 CA 2(CA 2+) FORMUL 7 2PE C18 H38 O10 FORMUL 8 PG4 C8 H18 O5 FORMUL 9 EDO 4(C2 H6 O2) FORMUL 13 ACT C2 H3 O2 1- FORMUL 14 ADP C10 H15 N5 O10 P2 FORMUL 15 ZN ZN 2+ FORMUL 16 HOH *143(H2 O) HELIX 1 1 THR A 441 LEU A 463 1 23 HELIX 2 2 LEU A 500 HIS A 509 1 10 HELIX 3 3 ASP A 517 PHE A 528 1 12 HELIX 4 4 GLU A 566 LEU A 570 5 5 HELIX 5 5 CYS A 586 SER A 592 1 7 HELIX 6 6 SER A 592 GLU A 606 1 15 HELIX 7 7 GLY A 623 LEU A 633 1 11 HELIX 8 8 ASN A 635 ASN A 661 1 27 HELIX 9 9 LEU A 671 ALA A 687 1 17 HELIX 10 10 LEU A 688 GLN A 692 5 5 HELIX 11 11 ASP A 703 THR A 717 1 15 SHEET 1 AA 5 ILE A 430 PHE A 437 0 SHEET 2 AA 5 ASN A 418 SER A 425 -1 O LEU A 419 N GLN A 436 SHEET 3 AA 5 LEU A 407 LEU A 414 -1 O ALA A 409 N VAL A 424 SHEET 4 AA 5 ARG A 466 THR A 474 1 O ARG A 466 N SER A 408 SHEET 5 AA 5 VAL A 512 ASN A 516 1 O TRP A 513 N ILE A 472 SHEET 1 AB 3 ARG A 477 ASN A 479 0 SHEET 2 AB 3 ILE A 484 HIS A 487 -1 O ILE A 484 N ASN A 479 SHEET 3 AB 3 VAL A 498 ASP A 499 -1 O VAL A 498 N VAL A 485 SHEET 1 AC 5 GLU A 555 LEU A 556 0 SHEET 2 AC 5 ILE A 546 HIS A 552 -1 O HIS A 552 N GLU A 555 SHEET 3 AC 5 PHE A 537 THR A 542 -1 O PHE A 537 N ILE A 551 SHEET 4 AC 5 LEU A 664 SER A 668 1 O LEU A 664 N VAL A 538 SHEET 5 AC 5 ASP A 695 VAL A 698 1 O ASP A 695 N VAL A 665 LINK OD2 ASP A 413 MG MG A1717 1555 1555 2.41 LINK OD1 ASN A 516 CA A CA A1719 1555 1555 2.52 LINK O GLY A 548 CA A CA A1719 1555 1555 2.51 LINK O ALA A 564 CA B CA A1719 1555 1555 2.79 LINK O ALA A 565 CA A CA A1719 1555 1555 2.57 LINK ND1 HIS A 569 ZN ZN A2000 1555 1555 2.13 LINK SG CYS A 579 ZN ZN A2000 1555 1555 2.37 LINK SG CYS A 581 ZN ZN A2000 1555 1555 2.29 LINK SG CYS A 586 ZN ZN A2000 1555 1555 2.24 LINK MG MG A1717 O1B ADP A1727 1555 1555 2.37 LINK MG MG A1717 O HOH A2002 1555 1555 2.44 LINK MG MG A1717 O HOH A2004 1555 1555 2.68 LINK MG MG A1717 O HOH A2142 1555 1555 2.26 LINK CA B CA A1719 O HOH A2046 1555 1555 2.53 LINK CA A CA A1719 O HOH A2066 1555 1555 2.53 CRYST1 90.700 90.700 101.490 90.00 90.00 90.00 P 41 21 2 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 0.011025 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011025 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009853 0.00000