MolNFT v1 · #119576 · protein
The crystal structure of a S-selective transaminase from bacillus megaterium bound with R-alpha-methylbenzylamine
5G09: “The crystal structure of a S-selective transaminase from bacillus megaterium bound with…”. X-ray diffraction, 1 ligand (6DF), 17 pockets (best druggability 0.86). MolNFT v1 #119576 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5G09
- Type
- protein
- Length
- 1,880 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transaminase
- EC
- 2.6.1.-
- Ligands
- 6DF
- Pockets
- 17 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Transaminase (EC 2.6.1.-) | protein | 468 | 39% helix, 18% strand | — |
| B | Transaminase (EC 2.6.1.-) | protein | 471 | 38% helix, 18% strand | — |
| D | Transaminase (EC 2.6.1.-) | protein | 473 | 38% helix, 18% strand | — |
Ligands and binding sites
- 6DF · [6-methyl-5-oxidanyl-4-[(~{E})-[(1~{R})-1-phenylethyl]iminomethyl]pyridin-3-yl]methyl dihydrogen phosphate · ligand · 4 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 8 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · 2 copies · chains C, D, A, B
- 1PE · Pentaethylene glycol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 772 | 0.86 | 0.89 | 102 | PGE |
| 2 | 727 | 0.83 | 0.86 | 71 | 6DF, PGE |
| 3 | 231 | 0.82 | 0.96 | 56 | empty |
| 4 | 759 | 0.82 | 0.85 | 74 | PGE, 6DF |
| 5 | 721 | 0.82 | 0.85 | 64 | 6DF, PGE |
Interfaces
6 interfaces between chains.
- A–B · 6023 Ų buried · 103 hydrogen bonds · protein-protein
- C–D · 5956 Ų buried · 100 hydrogen bonds · protein-protein
- A–D · 1589 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 1488 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 169 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5G09 · The crystal structure of a S-selective transaminase from Bacillus megaterium bound with… · 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 5G09 · PDBe 5G09
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