MolNFT v1 · #33523 · protein
Trypanosoma brucei udp-galactose-4-epimerase in ternary complex with NAD and the substrate analogue udp-4-deoxy-4- fluoro-alpha-D-galactose
2CNB: “Trypanosoma brucei udp-galactose-4-epimerase in ternary complex with NAD and the substrate analogue…”. X-ray diffraction, 2 ligands (UFG, NAD), 20 pockets (best druggability 0.85). MolNFT v1 #33523 on GenesisL1: 3D structure…
- PDB
- 2CNB
- Type
- protein
- Length
- 1,459 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-galactose-4-epimerase
- EC
- 5.1.3.2
- UniProt
- Q8T8E9
- Ligands
- UFG, NAD
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-galactose-4-epimerase (EC 5.1.3.2) | protein | 366 | 39% helix, 17% strand | Q8T8E9 |
| B | Udp-galactose-4-epimerase (EC 5.1.3.2) | protein | 363 | 40% helix, 17% strand | Q8T8E9 |
| C | Udp-galactose-4-epimerase (EC 5.1.3.2) | protein | 366 | 41% helix, 17% strand | Q8T8E9 |
| D | Udp-galactose-4-epimerase (EC 5.1.3.2) | protein | 364 | 42% helix, 18% strand | Q8T8E9 |
Ligands and binding sites
- UFG · Uridine-5'-diphosphate-4-deoxy-4-fluoro-alpha-D-galactose · ligand · 4 copies · chains A, B, C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 860 | 0.85 | 0.87 | 93 | UFG, NAD |
| 2 | 832 | 0.85 | 0.87 | 95 | UFG, NAD |
| 3 | 858 | 0.84 | 0.86 | 91 | UFG, NAD |
| 4 | 889 | 0.84 | 0.86 | 87 | UFG, NAD |
| 5 | 683 | 0.71 | 0.78 | 71 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1055 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1044 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 283 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 131 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2CNB · Trypanosoma brucei UDP-galactose-4-epimerase in ternary complex with NAD and the… · 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 Q8T8E9
- Elsewhere: RCSB PDB 2CNB · PDBe 2CNB · UniProt Q8T8E9
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