Research workbench
Crystal structure of a protein of unknown function ATU0492 from agrobacterium tumefaciens, putative antioxidant defence protein ahpd
Analyse Crystal structure of a protein of unknown function ATU0492 from agrobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GMY
- Type
- protein
- Length
- 876 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein ATU0492
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Hypothetical protein ATU0492 | protein | 147 | 74% helix, 0% strand | — |
| B | Hypothetical protein ATU0492 | protein | 146 | 74% helix, 0% strand | — |
| C | Hypothetical protein ATU0492 | protein | 146 | 73% helix, 0% strand | — |
| D, E | Hypothetical protein ATU0492 | protein | 145 | 76% helix, 0% strand | — |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.76 | 0.79 | 84 | empty |
| 2 | 525 | 0.68 | 0.78 | 46 | empty |
| 3 | 51 | 0.38 | 0.80 | 13 | empty |
| 4 | 51 | 0.36 | 0.79 | 14 | empty |
| 5 | 50 | 0.36 | 0.79 | 14 | empty |
Interfaces
12 interfaces between chains.
- C–D · 1817 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1770 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1762 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1161 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 1141 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2GMY · Crystal Structure of a Protein of Unknown Function ATU0492 from Agrobacterium… · 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 2GMY · PDBe 2GMY
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