MolNFT v1 · #47684 · protein
Crystal structure of thermus thermophilus HB8 udp-glucose 4-epimerase complex with NAD
2P5U: “Crystal structure of thermus thermophilus HB8 udp-glucose 4-epimerase complex with NAD”. X-ray diffraction, 1 ligand (NAD), 16 pockets (best druggability 0.81). MolNFT v1 #47684 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2P5U
- Type
- protein
- Length
- 1,244 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-glucose 4-epimerase
- EC
- 5.1.3.2
- UniProt
- Q5SKQ2
- Ligands
- NAD
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Udp-glucose 4-epimerase (EC 5.1.3.2) | protein | 311 | 42% helix, 18% strand | Q5SKQ2 |
Ligands and binding sites
- 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
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 472 | 0.81 | 0.89 | 58 | NAD |
| 2 | 392 | 0.79 | 0.88 | 50 | NAD |
| 3 | 402 | 0.79 | 0.88 | 55 | NAD |
| 4 | 369 | 0.77 | 0.87 | 47 | NAD |
| 5 | 332 | 0.72 | 0.84 | 35 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1215 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 1202 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 303 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 286 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2P5U · Crystal structure of Thermus thermophilus HB8 UDP-glucose 4-epimerase complex with NAD · 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 Q5SKQ2
- Elsewhere: RCSB PDB 2P5U · PDBe 2P5U · UniProt Q5SKQ2
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