Research workbench
Crystal structure of staphylococcus aureus cytidine monophosphate kinase in complex with cytidine-5'- monophosphate
Analyse Crystal structure of staphylococcus aureus cytidine monophosphate kinase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H92
- Type
- protein
- Length
- 648 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytidylate kinase
- EC
- 2.7.4.14
- UniProt
- Q1YBX2
- Ligands
- C5P, SO4
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Cytidylate kinase (EC 2.7.4.14) | protein | 216 | 50% helix, 16% strand | Q1YBX2 |
Ligands and binding sites
- C5P · Cytidine-5'-monophosphate · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1091 | 0.79 | 0.80 | 129 | SO4, C5P |
| 2 | 428 | 0.72 | 0.83 | 57 | SO4, C5P |
| 3 | 422 | 0.70 | 0.82 | 53 | SO4, C5P |
| 4 | 57 | 0.25 | 0.72 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–C · 538 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 420 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2H92 · Crystal Structure of Staphylococcus aureus Cytidine Monophosphate Kinase in complex with… · 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 Q1YBX2
- Elsewhere: RCSB PDB 2H92 · PDBe 2H92 · UniProt Q1YBX2
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