Research workbench
Crystal structure of a probable aminotransferase from pseudomonas aeruginosa
Analyse Crystal structure of a probable aminotransferase from pseudomonas aeruginosa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X5D
- Type
- protein
- Length
- 1,489 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable aminotransferase
- UniProt
- Q9HV83
- Ligands
- PLP, SO4
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable aminotransferase | protein | 371 | 48% helix, 15% strand | Q9HV83 |
| B | Probable aminotransferase | protein | 367 | 49% helix, 15% strand | Q9HV83 |
| C | Probable aminotransferase | protein | 371 | 49% helix, 15% strand | Q9HV83 |
| D | Probable aminotransferase | protein | 380 | 47% helix, 15% strand | Q9HV83 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, D
- SO4 · Sulfate ion · ion · 11 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.81 | 0.96 | 33 | SO4 |
| 2 | 1047 | 0.81 | 0.82 | 116 | SO4 |
| 3 | 160 | 0.79 | 0.95 | 45 | SO4 |
| 4 | 581 | 0.75 | 0.82 | 74 | PLP, SO4 |
| 5 | 645 | 0.71 | 0.79 | 61 | PLP |
Interfaces
4 interfaces between chains.
- A–D · 1602 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1478 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 937 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 913 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 cofactor (disulfide, pyridoxal phosphate Schiff base).
Compared structures
- 2X5D · Crystal Structure of a probable aminotransferase from Pseudomonas aeruginosa · 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 Q9HV83
- Elsewhere: RCSB PDB 2X5D · PDBe 2X5D · UniProt Q9HV83
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