MolNFT v1 · #88156 · protein
The (R)-selective transaminase from nectria haematococca
4CMD · Aminotransferase: “The (R)-selective transaminase from nectria haematococca”. X-ray diffraction, 1 ligand (PLP), 7 pockets (best druggability 0.75). MolNFT v1 #88156 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4CMD
- Type
- protein
- Length
- 644 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminotransferase
- EC
- 2.6.1.42
- UniProt
- C7YVL8
- Ligands
- PLP
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aminotransferase (EC 2.6.1.42) | protein | 322 | 34% helix, 27% strand | C7YVL8 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 394 | 0.75 | 0.85 | 51 | MES, PLP |
| 2 | 403 | 0.74 | 0.84 | 56 | MES, PLP |
| 3 | 136 | 0.58 | 0.83 | 23 | empty |
| 4 | 121 | 0.57 | 0.84 | 24 | empty |
| 5 | 78 | 0.44 | 0.81 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2387 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4CMD · The (R)-selective transaminase from Nectria haematococca · 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 C7YVL8
- Elsewhere: RCSB PDB 4CMD · PDBe 4CMD · UniProt C7YVL8
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