MolNFT v1 · #69698 · protein
Structure of udp-galactopyranose mutase bound to flavin mononucleotide
3KYB · Probable udp-galactopyranose mutase: “Structure of udp-galactopyranose mutase bound to flavin mononucleotide”. X-ray diffraction, 2 ligands (FMN, FAD), 4 pockets (best druggability 0.84). MolNFT v1 #69698 on GenesisL1: 3D structure…
- PDB
- 3KYB
- Type
- protein
- Length
- 764 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable udp-galactopyranose mutase
- EC
- 5.4.99.9
- UniProt
- Q48485
- Ligands
- FMN, FAD
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable udp-galactopyranose mutase (EC 5.4.99.9) | protein | 383 | 36% helix, 22% strand | Q48485 |
| B | Probable udp-galactopyranose mutase (EC 5.4.99.9) | protein | 381 | 35% helix, 22% strand | Q48485 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.84 | 0.84 | 97 | FAD, FMN |
| 2 | 1194 | 0.80 | 0.81 | 94 | FAD, FMN |
| 3 | 1062 | 0.76 | 0.79 | 68 | empty |
| 4 | 55 | 0.37 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1139 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3KYB · Structure of UDP-galactopyranose mutase bound to flavin mononucleotide · the same entry in another collection · chain A against A, TM-score 1.00
- Q48485 · AlphaFold monomer V2.0 prediction for udp-galactopyranose mutase (Q48485) · a predicted model of the same protein · chain A 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 Q48485
- Elsewhere: RCSB PDB 3KYB · PDBe 3KYB · UniProt Q48485
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