MolNFT v1 · #119650 · protein
The crystal structure of a S-selective transaminase from arthrobacter sp. with alanine bound
5G2Q: “The crystal structure of a S-selective transaminase from arthrobacter sp. with alanine bound”. X-ray diffraction, 1 ligand (PDA), 20 pockets (best druggability 0.89). MolNFT v1 #119650 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5G2Q
- Type
- protein
- Length
- 5,538 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transaminase
- EC
- 2.6.1.-
- Ligands
- PDA
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, I, J, K | Transaminase (EC 2.6.1.-) | protein | 461 | 39% helix, 18% strand | — |
| D, F | Transaminase (EC 2.6.1.-) | protein | 465 | 38% helix, 18% strand | — |
| G | Transaminase (EC 2.6.1.-) | protein | 459 | 39% helix, 18% strand | — |
| H | Transaminase (EC 2.6.1.-) | protein | 462 | 39% helix, 18% strand | — |
| L | Transaminase (EC 2.6.1.-) | protein | 460 | 38% helix, 17% strand | — |
Ligands and binding sites
- PDA · 2-[(3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl)-amino]-propionic acid · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.89 | 0.91 | 127 | empty |
| 2 | 1004 | 0.89 | 0.90 | 118 | empty |
| 3 | 481 | 0.83 | 0.90 | 71 | empty |
| 4 | 464 | 0.83 | 0.91 | 70 | empty |
| 5 | 603 | 0.82 | 0.87 | 68 | PDA |
Interfaces
19 interfaces between chains.
- E–F · 5778 Ų buried · 101 hydrogen bonds · protein-protein
- I–J · 5744 Ų buried · 100 hydrogen bonds · protein-protein
- C–D · 5741 Ų buried · 102 hydrogen bonds · protein-protein
- A–B · 5739 Ų buried · 97 hydrogen bonds · protein-protein
- G–H · 5694 Ų buried · 98 hydrogen bonds · protein-protein
Compared structures
- 5G2Q · The crystal structure of a S-selective transaminase from Arthrobacter sp. with alanine… · 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 5G2Q · PDBe 5G2Q
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