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The crystal structure of a S-selective transaminase from arthrobacter sp.
Analyse The crystal structure of a S-selective transaminase from arthrobacter sp. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5G2P
- Type
- protein
- Length
- 1,848 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transaminase
- EC
- 2.6.1.-
- Ligands
- PLP, CL
- Pockets
- 18 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transaminase (EC 2.6.1.-) | protein | 461 | 38% helix, 17% strand | — |
| B | Transaminase (EC 2.6.1.-) | protein | 464 | 38% helix, 17% strand | — |
| C | Transaminase (EC 2.6.1.-) | protein | 461 | 39% helix, 17% strand | — |
| D | Transaminase (EC 2.6.1.-) | protein | 462 | 39% helix, 18% strand | — |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 612 | 0.86 | 0.91 | 89 | empty |
| 2 | 701 | 0.82 | 0.86 | 79 | PLP |
| 3 | 704 | 0.82 | 0.85 | 73 | PLP |
| 4 | 683 | 0.82 | 0.86 | 72 | PLP |
| 5 | 678 | 0.82 | 0.86 | 67 | PLP |
Interfaces
4 interfaces between chains.
- C–D · 5715 Ų buried · 98 hydrogen bonds · protein-protein
- A–B · 5713 Ų buried · 100 hydrogen bonds · protein-protein
- B–D · 1296 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1255 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5G2P · The crystal structure of a S-selective transaminase from Arthrobacter sp. · 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
- Elsewhere: RCSB PDB 5G2P · PDBe 5G2P
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