Research workbench
Crystal structure of thermococcus kodakaraensis aconitase X (holo- form)
Analyse Crystal structure of thermococcus kodakaraensis aconitase X (holo- form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CNS
- Type
- protein
- Length
- 517 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DUF521 domain-containing protein; UPF0107 protein TK1248
- UniProt
- Q5JGJ6, Q5JGJ7
- Ligands
- PMV, F3S
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DUF521 domain-containing protein | protein | 386 | 45% helix, 17% strand | Q5JGJ6 |
| B | UPF0107 protein TK1248 | protein | 131 | 21% helix, 35% strand | Q5JGJ7 |
Ligands and binding sites
- PMV · (3R)-3-hydroxy-3-methyl-5-(phosphonooxy)pentanoic acid · ligand · chains A, B
- F3S · FE3-S4 cluster · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.79 | 0.97 | 30 | PMV, F3S |
| 2 | 266 | 0.62 | 0.80 | 24 | empty |
| 3 | 195 | 0.48 | 0.75 | 29 | empty |
| 4 | 67 | 0.35 | 0.77 | 13 | empty |
| 5 | 72 | 0.30 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1382 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 7CNS · Crystal structure of Thermococcus kodakaraensis aconitase X (holo-form) · the same entry in another collection · chain A against A, TM-score 1.00
- Q5JGJ7 · AlphaFold monomer V2.0 prediction for UPF0107 protein TK1248 (Q5JGJ7) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 7CNS · PDBe 7CNS · UniProt Q5JGJ6 · UniProt Q5JGJ7
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