MolNFT v1 · #164117 · protein
Crystal structure of the W60C mutant of the (S)-selective transaminase from chromobacterium violaceum
6SNU · Aspartate aminotransferase family protein: “Crystal structure of the W60C mutant of the (S)-selective transaminase from chromobacterium violaceum”. X-ray diffraction, 1 ligand (PLP), 13 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 6SNU
- Type
- protein
- Length
- 1,814 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate aminotransferase family protein
- EC
- 2.6.1.-
- UniProt
- A0A1R0MXM9
- Ligands
- PLP
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartate aminotransferase family protein (EC 2.6.1.-) | protein | 452 | 45% helix, 19% strand | A0A1R0MXM9 |
| B | Aspartate aminotransferase family protein (EC 2.6.1.-) | protein | 453 | 45% helix, 19% strand | A0A1R0MXM9 |
| C | Aspartate aminotransferase family protein (EC 2.6.1.-) | protein | 455 | 45% helix, 20% strand | A0A1R0MXM9 |
| D | Aspartate aminotransferase family protein (EC 2.6.1.-) | protein | 454 | 45% helix, 19% strand | A0A1R0MXM9 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 807 | 0.78 | 0.82 | 73 | empty |
| 2 | 637 | 0.77 | 0.82 | 70 | PLP |
| 3 | 668 | 0.76 | 0.82 | 70 | PLP |
| 4 | 577 | 0.74 | 0.81 | 71 | EDO, PLP |
| 5 | 614 | 0.74 | 0.80 | 72 | EDO, PLP |
Interfaces
3 interfaces between chains.
- C–D · 5473 Ų buried · 83 hydrogen bonds · protein-protein
- A–B · 5439 Ų buried · 81 hydrogen bonds · protein-protein
- B–C · 207 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 cofactor, 4 modified (pyridoxal phosphate Schiff base, oxidation).
Compared structures
- 6SNU · Crystal structure of the W60C mutant of the (S)-selective transaminase from… · 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 A0A1R0MXM9
- Elsewhere: RCSB PDB 6SNU · PDBe 6SNU · UniProt A0A1R0MXM9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.