MolNFT v1 · #167405 · protein
Oxygen tolerant archeal 4HYDROXYBUTYRYLCOA dehydratase (4HBD) from N. maritimus
6VJR · Vinylacetyl-CoA delta-isomerase: “Oxygen tolerant archeal 4HYDROXYBUTYRYLCOA dehydratase (4HBD) from N. maritimus”. X-ray diffraction, 5 ligands (SF4, FAD, FE), 20 pockets (best druggability 0.85). MolNFT v1 #167405 on GenesisL1: 3D…
- PDB
- 6VJR
- Type
- protein
- Length
- 2,003 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vinylacetyl-CoA delta-isomerase
- EC
- 5.3.3.3
- UniProt
- A9A1Y2
- Ligands
- SF4, FAD, FE, SO4, PO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vinylacetyl-CoA delta-isomerase (EC 5.3.3.3) | protein | 502 | 53% helix, 13% strand | A9A1Y2 |
| B | Vinylacetyl-CoA delta-isomerase (EC 5.3.3.3) | protein | 501 | 53% helix, 13% strand | A9A1Y2 |
| C, D | Vinylacetyl-CoA delta-isomerase (EC 5.3.3.3) | protein | 500 | 54% helix, 14% strand | A9A1Y2 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B, C, D
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, C, B, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, B, D
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1071 | 0.85 | 0.86 | 76 | SO4 |
| 2 | 758 | 0.79 | 0.83 | 75 | SF4, FAD |
| 3 | 761 | 0.78 | 0.82 | 76 | SF4, FAD |
| 4 | 736 | 0.77 | 0.82 | 72 | FAD, PO4 |
| 5 | 745 | 0.77 | 0.81 | 59 | FAD |
Interfaces
6 interfaces between chains.
- B–C · 3421 Ų buried · 42 hydrogen bonds · protein-protein
- A–D · 3400 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 3330 Ų buried · 47 hydrogen bonds · protein-protein
- B–D · 3323 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 52 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6VJR · Oxygen tolerant Archeal 4hydroxybutyrylCoA dehydratase (4HBD) from N. maritimus · 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 A9A1Y2
- Elsewhere: RCSB PDB 6VJR · PDBe 6VJR · UniProt A9A1Y2
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