MolNFT v1 · #168400 · protein
Streptomyces coelicolor methylmalonyl-CoA epimerase substrate complex
6WFH: “Streptomyces coelicolor methylmalonyl-CoA epimerase substrate complex”. X-ray diffraction, 4 ligands (V0V, CO, SO4), 1 pocket (best druggability 0.56). MolNFT v1 #168400 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6WFH
- Type
- protein
- Length
- 139 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylmalonyl-CoA epimerase
- UniProt
- Q9L2C2
- Ligands
- V0V, CO, SO4, CL
- Pockets
- 1 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylmalonyl-CoA epimerase | protein | 139 | 26% helix, 40% strand | Q9L2C2 |
Ligands and binding sites
- V0V · (3S,5R,9R,19E)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3, 5,9,19-tetrahydroxy-8,8,20-trimethyl-10,14-dioxo-2,4, 6-trioxa-18-thia-11,15-diaza-3,5-diphosphahenicos-19-en-21-oic acid 3,5-dioxide (non-preferred name) · ligand · chains A
- CO · Cobalt (II) ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
- CL · Chloride ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.56 | 0.86 | 23 | V0V |
Compared structures
- 6WFH · Streptomyces coelicolor methylmalonyl-CoA epimerase substrate complex · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9L2C2
- Elsewhere: RCSB PDB 6WFH · PDBe 6WFH · UniProt Q9L2C2
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