HEADER CARBOHYDRATE 08-FEB-23 8CHS TITLE HUMAN HEPARAN SULFATE N-DEACETYLASE-N-SULFOTRANSFERASE 1 IN COMPLEX TITLE 2 WITH CALCIUM, 3'-PHOSPHOADENOSINE-5'-PHOSPHOSULFATE AND NANOBODY TITLE 3 NAB13 (COMPOSITE MAP AND MODEL). COMPND MOL_ID: 1; COMPND 2 MOLECULE: NANOBODY NAB13 - ALL CA RIGID FIT MODEL DERIVED FROM COMPND 3 NANOBODY NAB7; COMPND 4 CHAIN: D; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: BIFUNCTIONAL HEPARAN SULFATE N-DEACETYLASE/N- COMPND 8 SULFOTRANSFERASE 1; COMPND 9 CHAIN: A; COMPND 10 SYNONYM: GLUCOSAMINYL N-DEACETYLASE/N-SULFOTRANSFERASE 1,NDST-1,N- COMPND 11 HEPARAN SULFATE SULFOTRANSFERASE 1,N-HSST 1,[HEPARAN SULFATE]- COMPND 12 GLUCOSAMINE N-SULFOTRANSFERASE 1,HSNST 1; COMPND 13 EC: 3.5.1.-,2.8.2.8; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 3 ORGANISM_TAXID: 9844; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_COMMON: HUMAN; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 GENE: NDST1, HSST, HSST1; SOURCE 11 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 7111 KEYWDS DEACETYLASE, SULFOTRANSFERASE, HEPARAN SULFATE, CARBOHYDRATE, KEYWDS 2 GLYCOSAMINOGLYCAN, NANOBODY EXPDTA ELECTRON MICROSCOPY AUTHOR C.J.MYCROFT-WEST,L.WU REVDAT 2 28-FEB-24 8CHS 1 JRNL REVDAT 1 21-FEB-24 8CHS 0 JRNL AUTH C.J.MYCROFT-WEST,S.ABDELKARIM,H.M.E.DUYVESTEYN,N.S.GANDHI, JRNL AUTH 2 M.A.SKIDMORE,R.J.OWENS,L.WU JRNL TITL STRUCTURAL AND MECHANISTIC CHARACTERIZATION OF BIFUNCTIONAL JRNL TITL 2 HEPARAN SULFATE N-DEACETYLASE-N-SULFOTRANSFERASE 1. JRNL REF NAT COMMUN V. 15 1326 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 38351061 JRNL DOI 10.1038/S41467-024-45419-4 REMARK 2 REMARK 2 RESOLUTION. 3.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EPU REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.150 REMARK 3 NUMBER OF PARTICLES : 87798 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: COMPOSITE MAP MADE BY COMBINING LOCALLY REFINED REMARK 3 VOLUMES OF NDST1 N-TERMINAL+DEACETYLASE, AND NDST1 DEACETYLASE+ REMARK 3 SULFOTRANSFERASE DOMAINS. RESOLUTION REPORTED FOR COMPOSITE MAP REMARK 3 IS THE RESOLUTION OF THE LOWEST LOCALLY REFINED COMPONENT. REMARK 4 REMARK 4 8CHS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1292128513. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : HUMAN HEPARAN SULFATE N REMARK 245 -DEACETYLASE-N-SULFOTRANSFERASE COMPLEX WITH NAB13; NANOBODY REMARK 245 NAB13 - ALL CA RIGID FIT MODEL DERIVED FROM NANOBODY NAB7; N- REMARK 245 DEACETYLASE-N-SULFOTRANSFERASE 1 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.40 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 6.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2600.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 165000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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 APPLY THE FOLLOWING TO CHAINS: D, 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 SER D 40 REMARK 465 PRO D 41 REMARK 465 GLY D 42 REMARK 465 LYS D 43 REMARK 465 ASP D 98 REMARK 465 ARG D 99 REMARK 465 SER D 100 REMARK 465 LYS D 101 REMARK 465 TYR D 102 REMARK 465 CYS D 103 REMARK 465 VAL D 104 REMARK 465 GLY D 105 REMARK 465 LYS D 106 REMARK 465 TYR D 107 REMARK 465 PHE D 108 REMARK 465 SER D 109 REMARK 465 THR D 110 REMARK 465 PRO D 111 REMARK 465 SER D 112 REMARK 465 GLN D 113 REMARK 465 TYR D 114 REMARK 465 ASP D 115 REMARK 465 PHE D 116 REMARK 465 SER D 126 REMARK 465 SER D 127 REMARK 465 GLU D 128 REMARK 465 PRO D 129 REMARK 465 LYS D 130 REMARK 465 THR D 131 REMARK 465 PRO D 132 REMARK 465 LYS D 133 REMARK 465 PRO D 134 REMARK 465 GLN D 135 REMARK 465 PRO D 136 REMARK 465 ALA D 137 REMARK 465 ALA D 138 REMARK 465 GLY D 139 REMARK 465 PRO D 140 REMARK 465 GLY D 141 REMARK 465 GLY D 142 REMARK 465 GLN D 143 REMARK 465 HIS D 144 REMARK 465 HIS D 145 REMARK 465 HIS D 146 REMARK 465 HIS D 147 REMARK 465 HIS D 148 REMARK 465 HIS D 149 REMARK 465 GLY D 150 REMARK 465 ALA D 151 REMARK 465 GLU D 152 REMARK 465 GLN D 153 REMARK 465 LYS D 154 REMARK 465 LEU D 155 REMARK 465 ILE D 156 REMARK 465 SER D 157 REMARK 465 GLU D 158 REMARK 465 GLU D 159 REMARK 465 ASP D 160 REMARK 465 LEU D 161 REMARK 465 SER D 162 REMARK 465 GLY A 78 REMARK 465 SER A 79 REMARK 465 ARG A 80 REMARK 465 THR A 81 REMARK 465 GLY A 118 REMARK 465 LYS A 119 REMARK 465 GLY A 120 REMARK 465 ASP A 121 REMARK 465 MET A 122 REMARK 465 LYS A 171 REMARK 465 ALA A 172 REMARK 465 ASN A 173 REMARK 465 GLU A 174 REMARK 465 ASN A 175 REMARK 465 SER A 176 REMARK 465 LEU A 177 REMARK 465 LEU A 178 REMARK 465 SER A 179 REMARK 465 ALA A 180 REMARK 465 GLN A 181 REMARK 465 LEU A 182 REMARK 465 LYS A 183 REMARK 465 GLY A 184 REMARK 465 PHE A 185 REMARK 465 PRO A 186 REMARK 465 LEU A 187 REMARK 465 PHE A 188 REMARK 465 LEU A 189 REMARK 465 HIS A 190 REMARK 465 SER A 191 REMARK 465 ASN A 192 REMARK 465 LEU A 193 REMARK 465 GLY A 194 REMARK 465 LEU A 195 REMARK 465 LYS A 196 REMARK 465 ASP A 197 REMARK 465 GLU A 214 REMARK 465 VAL A 215 REMARK 465 GLU A 216 REMARK 465 LYS A 217 REMARK 465 GLY A 218 REMARK 465 VAL A 219 REMARK 465 LEU A 220 REMARK 465 PRO A 221 REMARK 465 GLY A 222 REMARK 465 GLU A 223 REMARK 465 ASP A 224 REMARK 465 TRP A 225 REMARK 465 THR A 226 REMARK 465 VAL A 227 REMARK 465 PHE A 228 REMARK 465 GLN A 229 REMARK 465 SER A 230 REMARK 465 ASN A 231 REMARK 465 HIS A 232 REMARK 465 SER A 233 REMARK 465 ALA A 241 REMARK 465 LYS A 242 REMARK 465 THR A 243 REMARK 465 ARG A 244 REMARK 465 SER A 245 REMARK 465 SER A 246 REMARK 465 GLU A 247 REMARK 465 SER A 248 REMARK 465 ILE A 249 REMARK 465 PRO A 250 REMARK 465 HIS A 251 REMARK 465 LEU A 252 REMARK 465 GLY A 253 REMARK 465 ALA A 254 REMARK 465 ASP A 255 REMARK 465 ALA A 256 REMARK 465 GLY A 257 REMARK 465 LEU A 258 REMARK 465 HIS A 259 REMARK 465 ALA A 260 REMARK 465 ALA A 261 REMARK 465 LEU A 262 REMARK 465 GLN A 819 REMARK 465 LEU A 820 REMARK 465 LEU A 821 REMARK 465 GLU A 822 REMARK 465 GLY A 823 REMARK 465 GLY A 824 REMARK 465 LYS A 825 REMARK 465 THR A 826 REMARK 465 LYS A 827 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 D 1 CG CD OE1 NE2 REMARK 470 VAL D 2 CG1 CG2 REMARK 470 GLN D 3 CG CD OE1 NE2 REMARK 470 LEU D 4 CG CD1 CD2 REMARK 470 VAL D 5 CG1 CG2 REMARK 470 GLU D 6 CG CD OE1 OE2 REMARK 470 SER D 7 OG REMARK 470 SER D 11 OG REMARK 470 VAL D 12 CG1 CG2 REMARK 470 GLN D 13 CG CD OE1 NE2 REMARK 470 SER D 17 OG REMARK 470 LEU D 18 CG CD1 CD2 REMARK 470 ARG D 19 CG CD NE CZ NH1 NH2 REMARK 470 LEU D 20 CG CD1 CD2 REMARK 470 SER D 21 OG REMARK 470 CYS D 22 SG REMARK 470 SER D 25 OG REMARK 470 PHE D 27 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASN D 28 CG OD1 ND2 REMARK 470 VAL D 29 CG1 CG2 REMARK 470 ASP D 30 CG OD1 OD2 REMARK 470 ASP D 31 CG OD1 OD2 REMARK 470 TYR D 32 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ILE D 34 CG1 CG2 CD1 REMARK 470 TRP D 36 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP D 36 CZ3 CH2 REMARK 470 PHE D 37 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG D 38 CG CD NE CZ NH1 NH2 REMARK 470 GLN D 39 CG CD OE1 NE2 REMARK 470 GLU D 44 CG CD OE1 OE2 REMARK 470 ARG D 45 CG CD NE CZ NH1 NH2 REMARK 470 GLU D 46 CG CD OE1 OE2 REMARK 470 VAL D 48 CG1 CG2 REMARK 470 SER D 49 OG REMARK 470 CYS D 50 SG REMARK 470 ILE D 51 CG1 CG2 CD1 REMARK 470 ASP D 54 CG OD1 OD2 REMARK 470 THR D 56 OG1 CG2 REMARK 470 THR D 57 OG1 CG2 REMARK 470 TYR D 58 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 TYR D 59 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU D 60 CG CD OE1 OE2 REMARK 470 ASN D 61 CG OD1 ND2 REMARK 470 SER D 62 OG REMARK 470 VAL D 63 CG1 CG2 REMARK 470 LYS D 64 CG CD CE NZ REMARK 470 ARG D 66 CG CD NE CZ NH1 NH2 REMARK 470 PHE D 67 CG CD1 CD2 CE1 CE2 CZ REMARK 470 THR D 68 OG1 CG2 REMARK 470 VAL D 69 CG1 CG2 REMARK 470 SER D 70 OG REMARK 470 SER D 71 OG REMARK 470 ASP D 72 CG OD1 OD2 REMARK 470 LYS D 73 CG CD CE NZ REMARK 470 ARG D 74 CG CD NE CZ NH1 NH2 REMARK 470 ASP D 75 CG OD1 OD2 REMARK 470 ASN D 76 CG OD1 ND2 REMARK 470 THR D 77 OG1 CG2 REMARK 470 VAL D 78 CG1 CG2 REMARK 470 TYR D 79 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU D 80 CG CD1 CD2 REMARK 470 GLN D 81 CG CD OE1 NE2 REMARK 470 MET D 82 CG SD CE REMARK 470 ASN D 83 CG OD1 ND2 REMARK 470 ASN D 84 CG OD1 ND2 REMARK 470 LEU D 85 CG CD1 CD2 REMARK 470 ARG D 86 CG CD NE CZ NH1 NH2 REMARK 470 PRO D 87 CG CD REMARK 470 GLU D 88 CG CD OE1 OE2 REMARK 470 ASP D 89 CG OD1 OD2 REMARK 470 THR D 90 OG1 CG2 REMARK 470 ILE D 92 CG1 CG2 CD1 REMARK 470 TYR D 93 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 PHE D 94 CG CD1 CD2 CE1 CE2 CZ REMARK 470 CYS D 95 SG REMARK 470 TRP D 117 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP D 117 CZ3 CH2 REMARK 470 ARG D 119 CG CD NE CZ NH1 NH2 REMARK 470 THR D 121 OG1 CG2 REMARK 470 HIS D 122 CG ND1 CD2 CE1 NE2 REMARK 470 VAL D 123 CG1 CG2 REMARK 470 THR D 124 OG1 CG2 REMARK 470 VAL D 125 CG1 CG2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 LEU A 92 CA - CB - CG ANGL. DEV. = 16.6 DEGREES REMARK 500 VAL A 101 CG1 - CB - CG2 ANGL. DEV. = -11.1 DEGREES REMARK 500 LEU A 376 CA - CB - CG ANGL. DEV. = 14.6 DEGREES REMARK 500 ASP A 424 CB - CG - OD1 ANGL. DEV. = 6.8 DEGREES REMARK 500 PRO A 466 CA - N - CD ANGL. DEV. = -14.3 DEGREES REMARK 500 LEU A 516 CA - CB - CG ANGL. DEV. = 24.3 DEGREES REMARK 500 LEU A 558 CA - CB - CG ANGL. DEV. = 21.1 DEGREES REMARK 500 LEU A 561 CA - CB - CG ANGL. DEV. = 24.8 DEGREES REMARK 500 LEU A 561 CB - CG - CD2 ANGL. DEV. = 10.4 DEGREES REMARK 500 LEU A 566 CA - CB - CG ANGL. DEV. = 28.9 DEGREES REMARK 500 PRO A 754 CA - N - CD ANGL. DEV. = -15.9 DEGREES REMARK 500 ASP A 777 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 MET A 791 CA - CB - CG ANGL. DEV. = 13.8 DEGREES REMARK 500 MET A 791 CG - SD - CE ANGL. DEV. = 11.2 DEGREES REMARK 500 LEU A 862 CA - CB - CG ANGL. DEV. = 15.8 DEGREES 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 ALA D 91 -169.33 -167.05 REMARK 500 PRO A 83 49.54 -87.52 REMARK 500 ASN A 146 38.50 -97.85 REMARK 500 LEU A 239 63.57 -101.59 REMARK 500 LEU A 272 -38.39 -131.21 REMARK 500 ASN A 286 -35.66 -132.07 REMARK 500 PHE A 322 66.72 61.75 REMARK 500 LYS A 331 -163.76 -128.72 REMARK 500 PHE A 362 54.01 -94.80 REMARK 500 PRO A 612 -167.51 -79.20 REMARK 500 PHE A 640 -104.18 58.93 REMARK 500 GLN A 868 -168.10 -117.46 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 CA A 902 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 320 OD1 REMARK 620 2 ASP A 320 OD2 56.3 REMARK 620 3 HOH A1001 O 152.2 114.2 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8CCY RELATED DB: PDB REMARK 900 SAME PROTEIN WITHOUT NANOBODY REMARK 900 RELATED ID: 8CD0 RELATED DB: PDB REMARK 900 SAME PROTEIN WITH DIFFERENT NANOBODY NAB7 REMARK 900 RELATED ID: EMD-16664 RELATED DB: EMDB REMARK 900 HUMAN HEPARAN SULFATE N-DEACETYLASE-N-SULFOTRANSFERASE 1 IN COMPLEX REMARK 900 WITH MAGNESIUM, 3'-PHOSPHOADENOSINE-5'-PHOSPHOSULFATE AND NANOBODY REMARK 900 NAB13 (COMPOSITE MAP AND MODEL). REMARK 900 RELATED ID: 8CHS RELATED DB: PDB REMARK 900 MODEL FOR COMPOSITE MAP REMARK 900 RELATED ID: EMD-16661 RELATED DB: EMDB REMARK 900 CONSENSUS MAP REMARK 900 RELATED ID: EMD-16662 RELATED DB: EMDB REMARK 900 FOCUSSED REFINEMENT REMARK 900 RELATED ID: EMD-16663 RELATED DB: EMDB REMARK 900 FOCUSSED REFINEMENT DBREF 8CHS D 1 162 PDB 8CHS 8CHS 1 162 DBREF 8CHS A 79 882 UNP P52848 NDST1_HUMAN 79 882 SEQADV 8CHS GLY A 78 UNP P52848 EXPRESSION TAG SEQRES 1 D 162 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY SER VAL GLN SEQRES 2 D 162 ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 D 162 PHE ASN VAL ASP ASP TYR ALA ILE GLY TRP PHE ARG GLN SEQRES 4 D 162 SER PRO GLY LYS GLU ARG GLU GLY VAL SER CYS ILE GLY SEQRES 5 D 162 GLY ASP GLY THR THR TYR TYR GLU ASN SER VAL LYS GLY SEQRES 6 D 162 ARG PHE THR VAL SER SER ASP LYS ARG ASP ASN THR VAL SEQRES 7 D 162 TYR LEU GLN MET ASN ASN LEU ARG PRO GLU ASP THR ALA SEQRES 8 D 162 ILE TYR PHE CYS ALA ALA ASP ARG SER LYS TYR CYS VAL SEQRES 9 D 162 GLY LYS TYR PHE SER THR PRO SER GLN TYR ASP PHE TRP SEQRES 10 D 162 GLY ARG GLY THR HIS VAL THR VAL SER SER GLU PRO LYS SEQRES 11 D 162 THR PRO LYS PRO GLN PRO ALA ALA GLY PRO GLY GLY GLN SEQRES 12 D 162 HIS HIS HIS HIS HIS HIS GLY ALA GLU GLN LYS LEU ILE SEQRES 13 D 162 SER GLU GLU ASP LEU SER SEQRES 1 A 805 GLY SER ARG THR ASP PRO LEU VAL LEU VAL PHE VAL GLU SEQRES 2 A 805 SER LEU TYR SER GLN LEU GLY GLN GLU VAL VAL ALA ILE SEQRES 3 A 805 LEU GLU SER SER ARG PHE LYS TYR ARG THR GLU ILE ALA SEQRES 4 A 805 PRO GLY LYS GLY ASP MET PRO THR LEU THR ASP LYS GLY SEQRES 5 A 805 ARG GLY ARG PHE ALA LEU ILE ILE TYR GLU ASN ILE LEU SEQRES 6 A 805 LYS TYR VAL ASN LEU ASP ALA TRP ASN ARG GLU LEU LEU SEQRES 7 A 805 ASP LYS TYR CYS VAL ALA TYR GLY VAL GLY ILE ILE GLY SEQRES 8 A 805 PHE PHE LYS ALA ASN GLU ASN SER LEU LEU SER ALA GLN SEQRES 9 A 805 LEU LYS GLY PHE PRO LEU PHE LEU HIS SER ASN LEU GLY SEQRES 10 A 805 LEU LYS ASP CYS SER ILE ASN PRO LYS SER PRO LEU LEU SEQRES 11 A 805 TYR VAL THR ARG PRO SER GLU VAL GLU LYS GLY VAL LEU SEQRES 12 A 805 PRO GLY GLU ASP TRP THR VAL PHE GLN SER ASN HIS SER SEQRES 13 A 805 THR TYR GLU PRO VAL LEU LEU ALA LYS THR ARG SER SER SEQRES 14 A 805 GLU SER ILE PRO HIS LEU GLY ALA ASP ALA GLY LEU HIS SEQRES 15 A 805 ALA ALA LEU HIS ALA THR VAL VAL GLN ASP LEU GLY LEU SEQRES 16 A 805 HIS ASP GLY ILE GLN ARG VAL LEU PHE GLY ASN ASN LEU SEQRES 17 A 805 ASN PHE TRP LEU HIS LYS LEU VAL PHE VAL ASP ALA VAL SEQRES 18 A 805 ALA PHE LEU THR GLY LYS ARG LEU SER LEU PRO LEU ASP SEQRES 19 A 805 ARG TYR ILE LEU VAL ASP ILE ASP ASP ILE PHE VAL GLY SEQRES 20 A 805 LYS GLU GLY THR ARG MET LYS VAL GLU ASP VAL LYS ALA SEQRES 21 A 805 LEU PHE ASP THR GLN ASN GLU LEU ARG ALA HIS ILE PRO SEQRES 22 A 805 ASN PHE THR PHE ASN LEU GLY TYR SER GLY LYS PHE PHE SEQRES 23 A 805 HIS THR GLY THR ASN ALA GLU ASP ALA GLY ASP ASP LEU SEQRES 24 A 805 LEU LEU SER TYR VAL LYS GLU PHE TRP TRP PHE PRO HIS SEQRES 25 A 805 MET TRP SER HIS MET GLN PRO HIS LEU PHE HIS ASN GLN SEQRES 26 A 805 SER VAL LEU ALA GLU GLN MET ALA LEU ASN LYS LYS PHE SEQRES 27 A 805 ALA VAL GLU HIS GLY ILE PRO THR ASP MET GLY TYR ALA SEQRES 28 A 805 VAL ALA PRO HIS HIS SER GLY VAL TYR PRO VAL HIS VAL SEQRES 29 A 805 GLN LEU TYR GLU ALA TRP LYS GLN VAL TRP SER ILE ARG SEQRES 30 A 805 VAL THR SER THR GLU GLU TYR PRO HIS LEU LYS PRO ALA SEQRES 31 A 805 ARG TYR ARG ARG GLY PHE ILE HIS ASN GLY ILE MET VAL SEQRES 32 A 805 LEU PRO ARG GLN THR CYS GLY LEU PHE THR HIS THR ILE SEQRES 33 A 805 PHE TYR ASN GLU TYR PRO GLY GLY SER SER GLU LEU ASP SEQRES 34 A 805 LYS ILE ILE ASN GLY GLY GLU LEU PHE LEU THR VAL LEU SEQRES 35 A 805 LEU ASN PRO ILE SER ILE PHE MET THR HIS LEU SER ASN SEQRES 36 A 805 TYR GLY ASN ASP ARG LEU GLY LEU TYR THR PHE LYS HIS SEQRES 37 A 805 LEU VAL ARG PHE LEU HIS SER TRP THR ASN LEU ARG LEU SEQRES 38 A 805 GLN THR LEU PRO PRO VAL GLN LEU ALA GLN LYS TYR PHE SEQRES 39 A 805 GLN ILE PHE SER GLU GLU LYS ASP PRO LEU TRP GLN ASP SEQRES 40 A 805 PRO CYS GLU ASP LYS ARG HIS LYS ASP ILE TRP SER LYS SEQRES 41 A 805 GLU LYS THR CYS ASP ARG PHE PRO LYS LEU LEU ILE ILE SEQRES 42 A 805 GLY PRO GLN LYS THR GLY THR THR ALA LEU TYR LEU PHE SEQRES 43 A 805 LEU GLY MET HIS PRO ASP LEU SER SER ASN TYR PRO SER SEQRES 44 A 805 SER GLU THR PHE GLU GLU ILE GLN PHE PHE ASN GLY HIS SEQRES 45 A 805 ASN TYR HIS LYS GLY ILE ASP TRP TYR MET GLU PHE PHE SEQRES 46 A 805 PRO ILE PRO SER ASN THR THR SER ASP PHE TYR PHE GLU SEQRES 47 A 805 LYS SER ALA ASN TYR PHE ASP SER GLU VAL ALA PRO ARG SEQRES 48 A 805 ARG ALA ALA ALA LEU LEU PRO LYS ALA LYS VAL LEU THR SEQRES 49 A 805 ILE LEU ILE ASN PRO ALA ASP ARG ALA TYR SER TRP TYR SEQRES 50 A 805 GLN HIS GLN ARG ALA HIS ASP ASP PRO VAL ALA LEU LYS SEQRES 51 A 805 TYR THR PHE HIS GLU VAL ILE THR ALA GLY SER ASP ALA SEQRES 52 A 805 SER SER LYS LEU ARG ALA LEU GLN ASN ARG CYS LEU VAL SEQRES 53 A 805 PRO GLY TRP TYR ALA THR HIS ILE GLU ARG TRP LEU SER SEQRES 54 A 805 ALA TYR HIS ALA ASN GLN ILE LEU VAL LEU ASP GLY LYS SEQRES 55 A 805 LEU LEU ARG THR GLU PRO ALA LYS VAL MET ASP MET VAL SEQRES 56 A 805 GLN LYS PHE LEU GLY VAL THR ASN THR ILE ASP TYR HIS SEQRES 57 A 805 LYS THR LEU ALA PHE ASP PRO LYS LYS GLY PHE TRP CYS SEQRES 58 A 805 GLN LEU LEU GLU GLY GLY LYS THR LYS CYS LEU GLY LYS SEQRES 59 A 805 SER LYS GLY ARG LYS TYR PRO GLU MET ASP LEU ASP SER SEQRES 60 A 805 ARG ALA PHE LEU LYS ASP TYR TYR ARG ASP HIS ASN ILE SEQRES 61 A 805 GLU LEU SER LYS LEU LEU TYR LYS MET GLY GLN THR LEU SEQRES 62 A 805 PRO THR TRP LEU ARG GLU ASP LEU GLN ASN THR ARG HET A3P A 901 27 HET CA A 902 1 HETNAM A3P ADENOSINE-3'-5'-DIPHOSPHATE HETNAM CA CALCIUM ION FORMUL 3 A3P C10 H15 N5 O10 P2 FORMUL 4 CA CA 2+ FORMUL 5 HOH *(H2 O) HELIX 1 AA1 ARG D 86 THR D 90 5 5 HELIX 2 AA2 SER A 94 SER A 107 1 14 HELIX 3 AA3 ASN A 140 ASN A 146 1 7 HELIX 4 AA4 ASP A 148 GLY A 163 1 16 HELIX 5 AA5 PHE A 287 THR A 302 1 16 HELIX 6 AA6 LYS A 331 LEU A 345 1 15 HELIX 7 AA7 THR A 367 ASP A 375 1 9 HELIX 8 AA8 LEU A 376 SER A 379 5 4 HELIX 9 AA9 ASN A 401 HIS A 419 1 19 HELIX 10 AB1 HIS A 440 TRP A 451 1 12 HELIX 11 AB2 GLY A 501 ASN A 510 1 10 HELIX 12 AB3 GLY A 512 LEU A 520 1 9 HELIX 13 AB4 HIS A 529 TYR A 533 5 5 HELIX 14 AB5 ARG A 537 THR A 554 1 18 HELIX 15 AB6 PRO A 562 PHE A 574 1 13 HELIX 16 AB7 ASP A 588 TRP A 595 1 8 HELIX 17 AB8 GLY A 616 PHE A 623 1 8 HELIX 18 AB9 GLY A 648 LYS A 653 5 6 HELIX 19 AC1 GLY A 654 PHE A 661 1 8 HELIX 20 AC2 ALA A 678 PHE A 681 5 4 HELIX 21 AC3 GLU A 684 LEU A 694 1 11 HELIX 22 AC4 ASN A 705 HIS A 720 1 16 HELIX 23 AC5 ASP A 722 TYR A 728 1 7 HELIX 24 AC6 THR A 729 ILE A 734 1 6 HELIX 25 AC7 SER A 741 LEU A 752 1 12 HELIX 26 AC8 VAL A 753 GLY A 755 5 3 HELIX 27 AC9 TRP A 756 SER A 766 1 11 HELIX 28 AD1 GLY A 778 GLU A 784 1 7 HELIX 29 AD2 GLU A 784 GLY A 797 1 14 HELIX 30 AD3 ASP A 803 LEU A 808 1 6 HELIX 31 AD4 GLY A 830 GLY A 834 5 5 HELIX 32 AD5 ASP A 841 TYR A 852 1 12 HELIX 33 AD6 TYR A 852 MET A 866 1 15 HELIX 34 AD7 PRO A 871 ARG A 882 1 12 SHEET 1 AA1 4 GLN D 3 GLU D 6 0 SHEET 2 AA1 4 LEU D 18 SER D 25 -1 O ALA D 23 N VAL D 5 SHEET 3 AA1 4 THR D 77 MET D 82 -1 O VAL D 78 N CYS D 22 SHEET 4 AA1 4 THR D 68 ASP D 72 -1 N SER D 70 O TYR D 79 SHEET 1 AA2 5 THR D 57 TYR D 59 0 SHEET 2 AA2 5 GLU D 46 ILE D 51 -1 N CYS D 50 O TYR D 58 SHEET 3 AA2 5 GLY D 35 ARG D 38 -1 N ARG D 38 O GLU D 46 SHEET 4 AA2 5 ALA D 91 ALA D 96 -1 O PHE D 94 N PHE D 37 SHEET 5 AA2 5 THR D 121 VAL D 123 -1 O THR D 121 N TYR D 93 SHEET 1 AA3 7 TYR A 111 ILE A 115 0 SHEET 2 AA3 7 LEU A 84 VAL A 89 1 N VAL A 89 O GLU A 114 SHEET 3 AA3 7 PHE A 133 TYR A 138 1 O LEU A 135 N LEU A 86 SHEET 4 AA3 7 GLY A 165 PHE A 169 1 O GLY A 165 N ILE A 136 SHEET 5 AA3 7 ARG A 278 PHE A 281 1 O PHE A 281 N GLY A 168 SHEET 6 AA3 7 VAL A 266 ASP A 269 -1 N ASP A 269 O ARG A 278 SHEET 7 AA3 7 TYR A 235 PRO A 237 -1 N GLU A 236 O GLN A 268 SHEET 1 AA4 2 TYR A 313 LEU A 315 0 SHEET 2 AA4 2 ILE A 523 ILE A 525 1 O SER A 524 N LEU A 315 SHEET 1 AA5 3 ASP A 317 ILE A 321 0 SHEET 2 AA5 3 ASN A 355 TYR A 358 1 O GLY A 357 N ILE A 321 SHEET 3 AA5 3 TRP A 386 PHE A 387 1 O PHE A 387 N LEU A 356 SHEET 1 AA6 4 TYR A 427 ALA A 428 0 SHEET 2 AA6 4 VAL A 455 THR A 458 1 O SER A 457 N ALA A 428 SHEET 3 AA6 4 ILE A 478 PRO A 482 1 O LEU A 481 N THR A 456 SHEET 4 AA6 4 PHE A 473 HIS A 475 -1 N PHE A 473 O VAL A 480 SHEET 1 AA7 4 PHE A 674 LYS A 676 0 SHEET 2 AA7 4 LEU A 607 GLY A 611 1 N ILE A 609 O GLU A 675 SHEET 3 AA7 4 LYS A 698 LEU A 703 1 O LYS A 698 N LEU A 608 SHEET 4 AA7 4 VAL A 775 ASP A 777 1 O LEU A 776 N LEU A 703 SHEET 1 AA8 2 ALA A 809 PHE A 810 0 SHEET 2 AA8 2 TRP A 817 CYS A 818 -1 O CYS A 818 N ALA A 809 SSBOND 1 CYS A 586 CYS A 601 1555 1555 2.03 SSBOND 2 CYS A 818 CYS A 828 1555 1555 2.03 LINK OD1 ASP A 320 CA CA A 902 1555 1555 2.44 LINK OD2 ASP A 320 CA CA A 902 1555 1555 2.19 LINK CA CA A 902 O HOH A1001 1555 1555 2.13 CISPEP 1 TYR A 437 PRO A 438 0 3.85 CISPEP 2 TYR A 461 PRO A 462 0 -3.34 CISPEP 3 LYS A 465 PRO A 466 0 -1.73 CISPEP 4 GLY A 611 PRO A 612 0 0.60 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000