MolNFT v1 · #83132 · protein
Open form structure of cmp kinase in complex with cmp from thermus thermophilus HB8
3W8N · Cytidylate kinase: “Open form structure of cmp kinase in complex with cmp from thermus thermophilus HB8”. X-ray diffraction, 1 ligand (C5P), 2 pockets (best druggability 0.58). MolNFT v1 #83132 on GenesisL1: 3D structure, binding…
- PDB
- 3W8N
- Type
- protein
- Length
- 201 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytidylate kinase
- EC
- 2.7.4.25
- UniProt
- Q5SL35
- Ligands
- C5P
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytidylate kinase (EC 2.7.4.25) | protein | 201 | 48% helix, 16% strand | Q5SL35 |
Ligands and binding sites
- C5P · Cytidine-5'-monophosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.58 | 0.78 | 38 | C5P |
| 2 | 55 | 0.32 | 0.77 | 14 | empty |
Modifications
Observed in the structure: 2 modified (engineered).
Compared structures
- 3W8N · Open form structure of CMP kinase in complex with CMP from Thermus thermophilus HB8 · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SL35 · AlphaFold monomer V2.0 prediction for cytidylate kinase (Q5SL35) · a predicted model of the same protein · chain A against A, TM-score 0.70
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 Q5SL35
- Elsewhere: RCSB PDB 3W8N · PDBe 3W8N · UniProt Q5SL35
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