MolNFT v1 · #89202 · protein
Crystal structure of a cytidylate kinase cmk from mycobacterium abscessus bound to cytidine-5'-monophosphate
4DIE: “Crystal structure of a cytidylate kinase cmk from mycobacterium abscessus bound to cytidine-5'-monophosphate”. X-ray diffraction, 2 ligands (C5P, PO4), 4 pockets (best druggability 0.80). MolNFT v1 #89202 on GenesisL1: 3D structure…
- PDB
- 4DIE
- Type
- protein
- Length
- 818 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytidylate kinase
- EC
- 2.7.4.25
- UniProt
- B1MB31
- Ligands
- C5P, PO4
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytidylate kinase (EC 2.7.4.25) | protein | 204 | 50% helix, 16% strand | B1MB31 |
| B | Cytidylate kinase (EC 2.7.4.25) | protein | 201 | 47% helix, 16% strand | B1MB31 |
| C | Cytidylate kinase (EC 2.7.4.25) | protein | 213 | 49% helix, 15% strand | B1MB31 |
| D | Cytidylate kinase (EC 2.7.4.25) | protein | 200 | 47% helix, 16% strand | B1MB31 |
Ligands and binding sites
- C5P · Cytidine-5'-monophosphate · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1151 | 0.80 | 0.81 | 115 | C5P, PO4 |
| 2 | 547 | 0.77 | 0.84 | 68 | C5P |
| 3 | 300 | 0.69 | 0.84 | 40 | C5P |
| 4 | 309 | 0.64 | 0.80 | 28 | empty |
Interfaces
5 interfaces between chains.
- A–B · 628 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 611 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 518 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 187 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 65 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4DIE · Crystal structure of a cytidylate kinase CmK from Mycobacterium abscessus bound to… · 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 B1MB31
- Elsewhere: RCSB PDB 4DIE · PDBe 4DIE · UniProt B1MB31
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