MolNFT v1 · #96958 · protein
Carbamate kinase from giardia lamblia bound to AMP-pnp
4JZ7: “Carbamate kinase from giardia lamblia bound to AMP-pnp”. X-ray diffraction, 1 ligand (ANP), 6 pockets (best druggability 0.70). MolNFT v1 #96958 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4JZ7
- Type
- protein
- Length
- 1,202 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
- Ligands
- ANP
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Carbamate kinase (EC 2.7.2.2) | protein | 285 | 40% helix, 20% strand | A8BB85 |
| C, D | Carbamate kinase (EC 2.7.2.2) | protein | 316 | 36% helix, 22% strand | A8BB85 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.70 | 0.76 | 110 | ANP |
| 2 | 590 | 0.65 | 0.76 | 81 | ANP |
| 3 | 500 | 0.64 | 0.76 | 78 | ANP |
| 4 | 425 | 0.58 | 0.75 | 52 | ANP |
| 5 | 96 | 0.34 | 0.74 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2229 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2191 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 262 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 152 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 136 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4JZ7 · Carbamate kinase from Giardia lamblia bound to AMP-PNP · 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 4JZ7 · PDBe 4JZ7 · UniProt A8BB85
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