MolNFT v1 · #106113 · protein
Crystal structure of micobacterium tuberculosis udp-galactopyranose mutase in complex with substrate udp-galp
4RPG: “Crystal structure of micobacterium tuberculosis udp-galactopyranose mutase in complex with substrate udp-galp”. X-ray diffraction, 3 ligands (FAD, UDP, GDU), 11 pockets (best druggability 0.87). MolNFT v1 #106113 on GenesisL1: 3D…
- PDB
- 4RPG
- Type
- protein
- Length
- 1,177 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-galactopyranose mutase
- EC
- 5.4.99.9
- UniProt
- P9WIQ1
- Ligands
- FAD, UDP, GDU
- Pockets
- 11 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 392 | 38% helix, 19% strand | P9WIQ1 |
| A | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 393 | 39% helix, 19% strand | P9WIQ1 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 3 copies · chains B, A, C
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, C
- GDU · Galactose-uridine-5'-diphosphate · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 706 | 0.87 | 0.91 | 91 | FAD, UDP |
| 2 | 648 | 0.87 | 0.92 | 83 | FAD, GDU |
| 3 | 752 | 0.86 | 0.89 | 93 | FAD, UDP |
| 4 | 875 | 0.76 | 0.79 | 71 | empty |
| 5 | 408 | 0.66 | 0.79 | 38 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1112 Ų buried · 15 hydrogen bonds · protein-protein
- B–A · 497 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4RPG · Crystal structure of Micobacterium tuberculosis UDP-Galactopyranose mutase in complex… · the same entry in another collection · chain B against B, TM-score 1.00
- P9WIQ1 · AlphaFold monomer V2.0 prediction for udp-galactopyranose mutase (P9WIQ1) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 P9WIQ1
- Elsewhere: RCSB PDB 4RPG · PDBe 4RPG · UniProt P9WIQ1
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