Structure of PDB 6fxy Chain A Binding Site BS02

Receptor Information

>6fxy Chain A (length=700) Species: 9606 (Homo sapiens)

PVNPEKLLVITVATAETEGYLRFLRSAEFFNYTVRTLGLGEEWRGGDVAR
TVGGGQKVRWLKKEMEKYADREDMIIMFVDSYDVILAGSPTELLKKFVQS
GSRLLFSAESFCWPEWGLAEQYPEVGTGKRFLNSGGFIGFATTIHQIVRQ
WKYKDDDDDQLFYTRLYLDPGLREKLSLNLDHKSRIFQNLNGALDEVVLK
FDRNRVRIRNVAYDTLPIVVHGNGPTKLQLNYLGNYVPNGWTPEGGCGFC
NQDRQPPPRVFLAVFVEQPTPFLPRFLQRLLLLDYPPDRVTLFLHNNEVF
HEPHIADSWPQLQDHFSAVKLVGPEEALSPGEARDMAMDLCRQDPECEFY
FSLDADAVLTNLQTLRILIEENRKVIAPMLSRHGKLWSNFWGALSPDEYY
ARSEDYVELVQRKRVGVWNVPYISQAYVIRGDTLRMELPQRDVFSGSDTD
PDMAFCKSFRDKGIFLHLSNQHEFGRLLATSRYDTEHLHPDLWQIFDNPV
DWKEQYIHENYSRALEGEGIVEQPCPDVYWFPLLSEQMCDELVAEMEHYG
QWSGGRHEDSRLAGGYENVPTVDIHMKQVGYEDQWLQLLRTYVGPMTESL
FPGYHTKARAVMNFVVRYRPDEQPSLRPHHDSSTFTLNVALNHKGLDYEG
GGCRFLRYDCVISSPRKGWALLHPGRLTHYHEGLPTTWGTRYIMVSFVDP

Ligand information

• Ligand ID: UDP
• InChI: InChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
• InChIKey: XCCTYIAWTASOJW-XVFCMESISA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
  CACTVS 3.370: O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
  CACTVS 3.370: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
  OpenEye OEToolkits 1.7.0: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
  ACDLabs 12.01: O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
• Formula: C9 H14 N2 O12 P2
• Name: URIDINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL130266
• DrugBank: DB03435
• ZINC: ZINC000004490939
• PDB chain: 6fxy Chain A Residue 804

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6fxy Molecular architecture of the multifunctional collagen lysyl hydroxylase and glycosyltransferase LH3.
• Resolution: 2.138 Å
• Binding residue (original residue number in PDB): V44 A45 T46 W75 D112 S113 Y114 D115 G256 K259
• Binding residue (residue number reindexed from 1): V12 A13 T14 W43 D80 S81 Y82 D83 G224 K227
• Annotation score: 3

Enzymatic activity

• Enzyme Commision number: 1.14.11.4: procollagen-lysine 5-dioxygenase.
  2.4.1.50: procollagen galactosyltransferase.
  2.4.1.66: procollagen glucosyltransferase.

Gene Ontology

Molecular Function

• GO:0005506 iron ion binding
• GO:0005515 protein binding
• GO:0008475 procollagen-lysine 5-dioxygenase activity
• GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
• GO:0016757 glycosyltransferase activity
• GO:0031418 L-ascorbic acid binding
• GO:0033823 procollagen glucosyltransferase activity
• GO:0036094 small molecule binding
• GO:0046872 metal ion binding
• GO:0050211 procollagen galactosyltransferase activity
• GO:0051213 dioxygenase activity

Biological Process

• GO:0001701 in utero embryonic development
• GO:0001886 endothelial cell morphogenesis
• GO:0006493 protein O-linked glycosylation
• GO:0008104 protein localization
• GO:0017185 peptidyl-lysine hydroxylation
• GO:0021915 neural tube development
• GO:0030199 collagen fibril organization
• GO:0032963 collagen metabolic process
• GO:0042311 vasodilation
• GO:0046947 hydroxylysine biosynthetic process
• GO:0048730 epidermis morphogenesis
• GO:0060425 lung morphogenesis
• GO:0070831 basement membrane assembly

Cellular Component

• GO:0005576 extracellular region
• GO:0005615 extracellular space
• GO:0005783 endoplasmic reticulum
• GO:0005788 endoplasmic reticulum lumen
• GO:0005789 endoplasmic reticulum membrane
• GO:0005791 rough endoplasmic reticulum
• GO:0005794 Golgi apparatus
• GO:0005802 trans-Golgi network
• GO:0016020 membrane
• GO:0062023 collagen-containing extracellular matrix
• GO:0070062 extracellular exosome

External links

• PDB: RCSB:6fxy, PDBe:6fxy, PDBj:6fxy
• PDBsum: 6fxy
• PubMed: 30089812
• UniProt: O60568|PLOD3_HUMAN Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3 (Gene Name=PLOD3)