Research workbench
Crystal structure of cmp-kdo synthetase
Analyse Crystal structure of cmp-kdo synthetase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VH3
- Type
- protein
- Length
- 695 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-deoxy-manno-octulosonate cytidylyltransferase
- EC
- 2.7.7.38
- UniProt
- P44490
- Ligands
- CMK
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-deoxy-manno-octulosonate cytidylyltransferase (EC 2.7.7.38) | protein | 211 | 34% helix, 23% strand | P44490 |
| B | 3-deoxy-manno-octulosonate cytidylyltransferase (EC 2.7.7.38) | protein | 246 | 33% helix, 23% strand | P44490 |
| C | 3-deoxy-manno-octulosonate cytidylyltransferase (EC 2.7.7.38) | protein | 238 | 34% helix, 23% strand | P44490 |
Ligands and binding sites
- CMK · Cytidine 5'-monophosphate 3-deoxy-beta-D-gulo-oct-2-ulo-pyranosonic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 599 | 0.73 | 0.81 | 48 | CMK |
| 2 | 333 | 0.70 | 0.83 | 44 | empty |
| 3 | 230 | 0.56 | 0.78 | 27 | empty |
| 4 | 294 | 0.55 | 0.76 | 33 | CMK |
| 5 | 327 | 0.54 | 0.74 | 47 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1455 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 371 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 82 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
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 P44490
- Elsewhere: RCSB PDB 1VH3 · PDBe 1VH3 · UniProt P44490
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.