Research workbench
Crystal structure of Thermococcus kodakaraensis aconitase X (apo-form)
Analyse Crystal structure of Thermococcus kodakaraensis 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
- 7CNR
- Type
- protein
- Length
- 2,063 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.39
- Source
- Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
- Molecule
- DUF521 domain-containing protein; UPF0107 protein TK1248
- UniProt
- Q5JGJ6, Q5JGJ7
- Ligands
- F3S
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · resolution 3.39 · 4 distinct chains · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | DUF521 domain-containing protein | protein | 386 | 44% helix, 16% strand | Q5JGJ6 |
| B, H | UPF0107 protein TK1248 | protein | 131 | 16% helix, 30% strand | Q5JGJ7 |
| D | UPF0107 protein TK1248 | protein | 129 | 21% helix, 33% strand | Q5JGJ7 |
| F | UPF0107 protein TK1248 | protein | 128 | 18% helix, 28% strand | Q5JGJ7 |
Ligands and binding sites
- F3S · FE3-S4 cluster · ligand · 4 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 660 | 0.72 | 0.79 | 57 | F3S |
| 2 | 575 | 0.71 | 0.79 | 87 | empty |
| 3 | 569 | 0.71 | 0.79 | 65 | F3S |
| 4 | 307 | 0.70 | 0.84 | 41 | F3S |
| 5 | 517 | 0.70 | 0.80 | 66 | F3S |
Interfaces
8 interfaces between chains.
- E–G · 1651 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1616 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 981 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 972 Ų buried · 6 hydrogen bonds · protein-protein
- C–G · 945 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7CNR · Crystal structure of thermococcus kodakaraensis aconitase X (apo-form) · the same entry in another collection · chain H against H, TM-score 1.00
- Q5JGJ7 · AlphaFold monomer V2.0 prediction for UPF0107 protein TK1248 (Q5JGJ7) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 Q5JGJ6
- Every structure of UniProt Q5JGJ7
- Elsewhere: RCSB PDB 7CNR · PDBe 7CNR · UniProt Q5JGJ6 · UniProt Q5JGJ7
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