Research workbench
Carbamate kinase from giardia lamblia bound to citric acid
Analyse Carbamate kinase from giardia lamblia bound to citric acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JZ8
- Type
- protein
- Length
- 1,249 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbamate kinase
- EC
- 2.7.2.2
- UniProt
- A8BB85
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbamate kinase (EC 2.7.2.2) | protein | 316 | 39% helix, 24% strand | A8BB85 |
| B, C, D | Carbamate kinase (EC 2.7.2.2) | protein | 311 | 40% helix, 24% strand | A8BB85 |
Ligands and binding sites
- CIT · Citric acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 980 | 0.84 | 0.85 | 131 | CIT |
| 2 | 948 | 0.80 | 0.82 | 83 | CIT |
| 3 | 551 | 0.76 | 0.83 | 72 | CIT |
| 4 | 604 | 0.74 | 0.81 | 74 | CIT |
| 5 | 54 | 0.30 | 0.76 | 18 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2234 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2180 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 531 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 339 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 287 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4JZ8 · Carbamate kinase from Giardia lamblia bound to citric acid · 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 A8BB85
- Elsewhere: RCSB PDB 4JZ8 · PDBe 4JZ8 · UniProt A8BB85
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