MolNFT v1 · #73725 · protein
Crystal structure of cytidylyltransferase from vibrio cholerae
3OAM · 3-deoxy-manno-octulosonate cytidylyltransferase: “Crystal structure of cytidylyltransferase from vibrio cholerae”. X-ray diffraction, 1 ligand (NA), 13 pockets (best druggability 0.79). MolNFT v1 #73725 on GenesisL1: 3D structure…
- PDB
- 3OAM
- Type
- protein
- Length
- 1,004 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-deoxy-manno-octulosonate cytidylyltransferase
- EC
- 2.7.7.38
- UniProt
- Q9KQX2
- Ligands
- NA
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-deoxy-manno-octulosonate cytidylyltransferase (EC 2.7.7.38) | protein | 252 | 35% helix, 23% strand | Q9KQX2 |
| B, C | 3-deoxy-manno-octulosonate cytidylyltransferase (EC 2.7.7.38) | protein | 251 | 33% helix, 23% strand | Q9KQX2 |
| D | 3-deoxy-manno-octulosonate cytidylyltransferase (EC 2.7.7.38) | protein | 250 | 34% helix, 24% strand | Q9KQX2 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 798 | 0.79 | 0.83 | 89 | empty |
| 2 | 73 | 0.68 | 0.94 | 17 | empty |
| 3 | 633 | 0.65 | 0.75 | 53 | empty |
| 4 | 493 | 0.61 | 0.75 | 49 | empty |
| 5 | 437 | 0.59 | 0.75 | 48 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1322 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1301 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 427 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 226 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 203 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3OAM · Crystal structure of cytidylyltransferase from Vibrio cholerae · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KQX2 · AlphaFold monomer V2.0 prediction for 3-deoxy-manno-octulosonate cytidylyltransferase… · a predicted model of the same protein · chain D against A, TM-score 0.98
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 Q9KQX2
- Elsewhere: RCSB PDB 3OAM · PDBe 3OAM · UniProt Q9KQX2
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