MolNFT v1 · #55004 · protein
Evidence for a two-metal-ion-mechanism in the kdo- cytidylyltransferase kdsb
2Y6P · 3-deoxy-manno-octulosonate cytidylyltransferase: “Evidence for a two-metal-ion-mechanism in the kdo- cytidylyltransferase kdsb”. X-ray diffraction, 2 ligands (CTP, MG), 6 pockets (best druggability 0.75). MolNFT v1 #55004 on…
- PDB
- 2Y6P
- Type
- protein
- Length
- 693 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
- O66914
- Ligands
- CTP, MG
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-deoxy-manno-octulosonate cytidylyltransferase (EC 2.7.7.38) | protein | 231 | 33% helix, 23% strand | O66914 |
| B | 3-deoxy-manno-octulosonate cytidylyltransferase (EC 2.7.7.38) | protein | 233 | 31% helix, 23% strand | O66914 |
| C | 3-deoxy-manno-octulosonate cytidylyltransferase (EC 2.7.7.38) | protein | 229 | 31% helix, 24% strand | O66914 |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 6 copies · chains A, B, C
- IPA · Isopropyl alcohol · additive · 2 copies · chains A, C
- BME · Beta-mercaptoethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 735 | 0.75 | 0.80 | 58 | CTP, MG, IPA |
| 2 | 690 | 0.74 | 0.80 | 57 | CTP, MG |
| 3 | 609 | 0.72 | 0.80 | 47 | CTP, MG, IPA |
| 4 | 926 | 0.71 | 0.76 | 70 | empty |
| 5 | 137 | 0.63 | 0.86 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1396 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 332 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 125 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2Y6P · Evidence for a Two-Metal-Ion-Mechanism in the Kdo- Cytidylyltransferase KdsB · the same entry in another collection · chain A against A, TM-score 1.00
- O66914 · AlphaFold monomer V2.0 prediction for 3-deoxy-manno-octulosonate cytidylyltransferase… · a predicted model of the same protein · chain C against A, TM-score 0.99
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 O66914
- Elsewhere: RCSB PDB 2Y6P · PDBe 2Y6P · UniProt O66914
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.