Research workbench
X-ray crystal structure of S. venezuelae desv in complex with ketimine intermediate
Analyse X-ray crystal structure of S. venezuelae desv in complex with ketimine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OGA
- Type
- protein
- Length
- 1,480 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transaminase
- UniProt
- Q9ZGH4
- Ligands
- PGU, NA, CL
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transaminase | protein | 371 | 42% helix, 15% strand | Q9ZGH4 |
| B, D | Transaminase | protein | 370 | 42% helix, 16% strand | Q9ZGH4 |
| C | Transaminase | protein | 369 | 42% helix, 15% strand | Q9ZGH4 |
Ligands and binding sites
- PGU · N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-glutamic acid · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 2 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.77 | 0.89 | 45 | CL, PGU |
| 2 | 298 | 0.75 | 0.87 | 46 | CL, PGU |
| 3 | 437 | 0.73 | 0.83 | 54 | PGU, CL |
| 4 | 408 | 0.73 | 0.83 | 49 | PGU, CL |
| 5 | 398 | 0.68 | 0.81 | 39 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2262 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 2242 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 412 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 280 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 273 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2OGA · X-ray crystal structure of S. venezuelae DesV in complex with ketimine intermediate · the same entry in another collection · chain B against B, TM-score 1.00
- Q9ZGH4 · AlphaFold monomer V2.0 prediction for dtdp-3-amino-3,4,6-trideoxy- alpha-D-glucose… · a predicted model of the same protein · chain B 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 Q9ZGH4
- Elsewhere: RCSB PDB 2OGA · PDBe 2OGA · UniProt Q9ZGH4
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