Research workbench
X-ray structure of S. venezuelae desv in its internal aldimine form
Analyse X-ray structure of S. venezuelae desv in its internal aldimine form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OGE
- Type
- protein
- Length
- 1,474 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transaminase
- UniProt
- Q9ZGH4
- Ligands
- NA, CL
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Transaminase | protein | 368 | 42% helix, 16% strand | Q9ZGH4 |
| B, C | Transaminase | protein | 369 | 43% helix, 16% strand | Q9ZGH4 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B, C, D
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 21 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 432 | 0.76 | 0.85 | 39 | CL, EDO |
| 2 | 492 | 0.74 | 0.83 | 39 | EDO, CL |
| 3 | 347 | 0.74 | 0.85 | 40 | CL, EDO |
| 4 | 457 | 0.73 | 0.83 | 39 | EDO, CL |
| 5 | 254 | 0.65 | 0.82 | 37 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2235 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 2219 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 435 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 292 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 199 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 2OGE · x-ray structure of S. venezuelae DesV in its internal aldimine form · the same entry in another collection · chain D against D, 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 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 Q9ZGH4
- Elsewhere: RCSB PDB 2OGE · PDBe 2OGE · UniProt Q9ZGH4
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