Structure of PDB 6fxk Chain A Binding Site BS01

Receptor Information
>6fxk Chain A (length=670) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PVNPEKLLVITVATAETEGYLRFLRSAEFFNYTVRTLGLGQKVRWLKKEM
EKYADREDMIIMFVDSYDVILAGSPTELLKKFVQSGSRLLFSAESFCWPE
WGLAEQYPEVGTGKRFLNSGGFIGFATTIHQIVRQWKYKDDDDDQLFYTR
LYLDPGLREKLSLNLDHKSRIFQNLNGALDEVVLKFDRNRVRIRNVAYDT
LPIVVHGNGPTKLQLNYLGNYVPNGWTPEGGCGFCNQDQPPPRVFLAVFV
EQPTPFLPRFLQRLLLLDYPPDRVTLFLHNNEVFHEPHIADSWPQLQDHF
SAVKLVGPEEALSPGEARDMAMDLCRQDPECEFYFSLDADAVLTNLQTLR
ILIEENRKVIAPMLSRHGKLWSNFWGALSPDEYYARSEDYVELVQRKRVG
VWNVPYISQAYVIRGDTLRMELPQRDVFSGSDTDPDMAFCKSFRDKGIFL
HLSNQHEFGRLLATSRYDTEHLHPDLWQIFDNPVDWKEQYIHENYSRALE
GEGIVEQPCPDVYWFPLLSEQMCDELVAEMEHYGQWSNVPTVDIHMKQVG
YEDQWLQLLRTYVGPMTESLFPGYHTKARAVMNFVVRYRPDEQPSLRPHH
DSSTFTLNVALNHKGLDYEGGGCRFLRYDCVISSPRKGWALLHPGRLTHY
HEGLPTTWGTRYIMVSFVDP
Ligand information
Ligand IDAKG
InChIInChI=1S/C5H6O5/c6-3(5(9)10)1-2-4(7)8/h1-2H2,(H,7,8)(H,9,10)
InChIKeyKPGXRSRHYNQIFN-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)C(=O)CCC(=O)O
OpenEye OEToolkits 1.7.6C(CC(=O)O)C(=O)C(=O)O
CACTVS 3.385OC(=O)CCC(=O)C(O)=O
FormulaC5 H6 O5
Name2-OXOGLUTARIC ACID
ChEMBLCHEMBL1686
DrugBankDB08845
ZINCZINC000001532519
PDB chain6fxk Chain A Residue 803 [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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PDB6fxk Molecular architecture of the multifunctional collagen lysyl hydroxylase and glycosyltransferase LH3.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		Y656 H667 C691 H719 R729
Binding residue
(residue number reindexed from 1)		Y588 H599 C623 H651 R661
Annotation score5
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
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Cellular Component
External links
PDB RCSB:6fxk, PDBe:6fxk, PDBj:6fxk
PDBsum6fxk
PubMed30089812
UniProtO60568|PLOD3_HUMAN Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3 (Gene Name=PLOD3)

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