Structure of PDB 6tez Chain A Binding Site BS01

Receptor Information
>6tez Chain A (length=697) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PVNPEKLLVITVATAETEGYLRFLRSAEFFNYTVRTLGLGEEWRGGDTVG
GGQKVRWLKKEMEKYADREDMIIMFVDSYDVILAGSPTELLKKFVQSGSR
LLFSAESFCWPEWGLAEQYPEVGTGKRFLNSGGFIGFATTIHQIVRQWKY
KDDDDDQLFYTRLYLDPGLREKLSLNLDHKSRIFQNLNGALDEVVLKFDR
NRVRIRNVAYDTLPIVVHGNGPTKLQLNYLGNYVPNGWTPEGGCGFCNQD
RQPPPRVFLAVFVEQPTPFLPRFLQRLLLLDYPPDRVTLFLHNNEVFHEP
HIADSWPQLQDHFSAVKLVGPEEALSPGEARDMAMDLCRQDPECEFYFSL
DADAVLTNLQTLRILIEENRKVIAPMLSRHGKLWSNFWGALSPDEYYARS
EDYVELVQRKRVGVWNVPYISQAYVIRGDTLRMELPQRDVFSGSDTDPDM
AFCKSFRDKGIFLHLSNQHEFGRLLATSRYDTEHLHPDLWQIFDNPVDWK
EQYIHENYSRALEGEGIVEQPCPDVYWFPLLSEQMCDELVAEMEHYGQWS
GGRHEDSRLAGGYENVPTVDIHMKQVGYEDQWLQLLRTYVGPMTESLFPG
YHTKARAVMNFVVRYRPDEQPSLRPHHDSSTFTLNVALNHKGLDYEGGGC
RFLRYDCVISSPRKGWALLHPGRLTHYHEGLPTTWGTRYIMVSFVDP
Ligand information
Ligand IDUGA
InChIInChI=1S/C15H22N2O18P2/c18-5-1-2-17(15(26)16-5)12-9(22)6(19)4(32-12)3-31-36(27,28)35-37(29,30)34-14-10(23)7(20)8(21)11(33-14)13(24)25/h1-2,4,6-12,14,19-23H,3H2,(H,24,25)(H,27,28)(H,29,30)(H,16,18,26)/t4-,6-,7+,8+,9-,10-,11+,12-,14-/m1/s1
InChIKeyHDYANYHVCAPMJV-LXQIFKJMSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)C3OC(OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O)C(O)C(O)C3O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]([CH]1O)C(O)=O)O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@@](=O)(O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)C(=O)O)O)O)O)O)O
CACTVS 3.341O[C@@H]1[C@@H](O)[C@H](O[C@@H]([C@H]1O)C(O)=O)O[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)C(=O)O)O)O)O)O)O
FormulaC15 H22 N2 O18 P2
NameURIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID;
UDP-GLUCURONIC ACID
ChEMBLCHEMBL228057
DrugBankDB03041
ZINCZINC000008215691
PDB chain6tez Chain A Residue 801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6tez Identification of Regulatory Molecular 'Hot Spots' for LH/PLOD Collagen Glycosyltransferase Activity
Resolution2.7 Å
Binding residue
(original residue number in PDB)		V44 A45 T46 W75 T83 G85 D112 Y114 D115 W145 H253 K259
Binding residue
(residue number reindexed from 1)		V12 A13 T14 W43 T48 G50 D77 Y79 D80 W110 H218 K224
Annotation score3
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

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6tez, PDBe:6tez, PDBj:6tez
PDBsum6tez
PubMed
UniProtO60568|PLOD3_HUMAN Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3 (Gene Name=PLOD3)

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