Research workbench
Crystal structure of Agrobacterium tumefaciens aconitase X (apo-form)
Analyse Crystal structure of Agrobacterium tumefaciens aconitase X (apo-form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CNP
- Type
- protein
- Length
- 1,675 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.6
- Source
- Agrobacterium tumefaciens
- Molecule
- cis-3-hydroxy-L-proline dehydratase
- Ligands
- FES, MG
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · resolution 1.6 · 2 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | cis-3-hydroxy-L-proline dehydratase | protein | 559 | 37% helix, 18% strand | — |
| B, C | cis-3-hydroxy-L-proline dehydratase | protein | 558 | 38% helix, 18% strand | — |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1191 | 0.78 | 0.80 | 122 | empty |
| 2 | 676 | 0.69 | 0.77 | 80 | empty |
| 3 | 331 | 0.66 | 0.81 | 31 | empty |
| 4 | 325 | 0.65 | 0.81 | 34 | empty |
| 5 | 270 | 0.64 | 0.81 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–B · 572 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 342 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 169 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7CNP · Crystal structure of agrobacterium tumefaciens aconitase X (apo-form) · 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 7CNP · PDBe 7CNP
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