Research workbench
Crystal structure of the omega transaminase from chromobacterium violaceum in complex with pmp
Analyse Crystal structure of the omega transaminase from chromobacterium violaceum in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S4G
- Type
- protein
- Length
- 1,815 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable aminotransferase
- EC
- 2.6.1.62
- UniProt
- Q7NWG4
- Ligands
- PMP
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable aminotransferase (EC 2.6.1.62) | protein | 453 | 45% helix, 19% strand | Q7NWG4 |
| C | Probable aminotransferase (EC 2.6.1.62) | protein | 455 | 45% helix, 19% strand | Q7NWG4 |
| D | Probable aminotransferase (EC 2.6.1.62) | protein | 454 | 45% helix, 19% strand | Q7NWG4 |
Ligands and binding sites
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 821 | 0.78 | 0.82 | 75 | empty |
| 2 | 617 | 0.74 | 0.81 | 74 | PMP, EDO |
| 3 | 537 | 0.74 | 0.82 | 61 | PMP, PEG |
| 4 | 636 | 0.73 | 0.80 | 69 | PMP, EDO, PEG |
| 5 | 619 | 0.73 | 0.80 | 72 | PMP, EDO |
Interfaces
3 interfaces between chains.
- C–D · 5456 Ų buried · 85 hydrogen bonds · protein-protein
- A–B · 5418 Ų buried · 84 hydrogen bonds · protein-protein
- B–C · 178 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6S4G · Crystal structure of the omega transaminase from Chromobacterium violaceum in 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 Q7NWG4
- Elsewhere: RCSB PDB 6S4G · PDBe 6S4G · UniProt Q7NWG4
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