Research workbench
Structure of giardia carbamate kinase
Analyse Structure of giardia carbamate kinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KZF
- Type
- protein
- Length
- 1,163 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
- 12 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbamate kinase (EC 2.7.2.2) | protein | 285 | 40% helix, 19% strand | A8BB85 |
| B | Carbamate kinase (EC 2.7.2.2) | protein | 298 | 39% helix, 19% strand | A8BB85 |
| C | Carbamate kinase (EC 2.7.2.2) | protein | 287 | 40% helix, 20% strand | A8BB85 |
| D | Carbamate kinase (EC 2.7.2.2) | protein | 293 | 38% helix, 19% strand | A8BB85 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains B, D, C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 724 | 0.78 | 0.82 | 65 | empty |
| 2 | 683 | 0.67 | 0.75 | 66 | empty |
| 3 | 470 | 0.66 | 0.78 | 50 | GOL |
| 4 | 587 | 0.66 | 0.76 | 69 | GOL |
| 5 | 504 | 0.65 | 0.77 | 71 | GOL |
Interfaces
5 interfaces between chains.
- A–B · 2166 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 539 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 402 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 337 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 42 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3KZF · Structure of Giardia Carbamate Kinase · 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 3KZF · PDBe 3KZF · UniProt A8BB85
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