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Crystal structure of an engineered sitagliptin-producing transaminase, ata-117-RD11
Analyse Crystal structure of an engineered sitagliptin-producing transaminase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WWJ
- Type
- protein
- Length
- 3,848 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- (R)-amine transaminase
- EC
- 2.1.6.18
- UniProt
- F7J696
- Ligands
- PLP
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 27% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, I, K | (R)-amine transaminase (EC 2.1.6.18) | protein | 320 | 27% helix, 27% strand | F7J696 |
| B | (R)-amine transaminase (EC 2.1.6.18) | protein | 323 | 28% helix, 26% strand | F7J696 |
| C, E, G, H | (R)-amine transaminase (EC 2.1.6.18) | protein | 321 | 27% helix, 26% strand | F7J696 |
| D, F | (R)-amine transaminase (EC 2.1.6.18) | protein | 322 | 27% helix, 26% strand | F7J696 |
| J | (R)-amine transaminase (EC 2.1.6.18) | protein | 319 | 28% helix, 27% strand | F7J696 |
| L | (R)-amine transaminase (EC 2.1.6.18) | protein | 318 | 27% helix, 26% strand | F7J696 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · 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 | 472 | 0.81 | 0.88 | 49 | PLP |
| 2 | 545 | 0.81 | 0.87 | 59 | PLP |
| 3 | 502 | 0.80 | 0.87 | 51 | PLP |
| 4 | 480 | 0.80 | 0.87 | 51 | PLP |
| 5 | 510 | 0.80 | 0.87 | 51 | PLP |
Interfaces
22 interfaces between chains.
- J–L · 2395 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2389 Ų buried · 45 hydrogen bonds · protein-protein
- I–K · 2387 Ų buried · 41 hydrogen bonds · protein-protein
- G–H · 2373 Ų buried · 41 hydrogen bonds · protein-protein
- D–F · 2372 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 1 disulfide (oxidation, disulfide).
Compared structures
- 3WWJ · Crystal structure of an engineered sitagliptin-producing transaminase, ATA-117-Rd11 · 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 F7J696
- Elsewhere: RCSB PDB 3WWJ · PDBe 3WWJ · UniProt F7J696
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