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The crystal structure of udp-N-acetylglucosamine 4-epimerase from bacillus cereus
Analyse The crystal structure of udp-N-acetylglucosamine 4-epimerase from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M2P
- Type
- protein
- Length
- 1,640 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylglucosamine 4-epimerase
- EC
- 5.1.3.7
- UniProt
- Q814Z6
- Ligands
- UDP
- Pockets
- 16 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylglucosamine 4-epimerase (EC 5.1.3.7) | protein | 287 | 39% helix, 21% strand | Q814Z6 |
| B | Udp-N-acetylglucosamine 4-epimerase (EC 5.1.3.7) | protein | 255 | 44% helix, 21% strand | Q814Z6 |
| C | Udp-N-acetylglucosamine 4-epimerase (EC 5.1.3.7) | protein | 280 | 42% helix, 20% strand | Q814Z6 |
| D | Udp-N-acetylglucosamine 4-epimerase (EC 5.1.3.7) | protein | 289 | 39% helix, 20% strand | Q814Z6 |
| E | Udp-N-acetylglucosamine 4-epimerase (EC 5.1.3.7) | protein | 262 | 43% helix, 19% strand | Q814Z6 |
| F | Udp-N-acetylglucosamine 4-epimerase (EC 5.1.3.7) | protein | 267 | 43% helix, 19% strand | Q814Z6 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · chains B
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 | 1005 | 0.87 | 0.89 | 115 | empty |
| 2 | 535 | 0.70 | 0.79 | 52 | empty |
| 3 | 417 | 0.70 | 0.81 | 47 | empty |
| 4 | 638 | 0.69 | 0.78 | 47 | empty |
| 5 | 589 | 0.69 | 0.78 | 58 | UDP |
Interfaces
12 interfaces between chains.
- D–E · 1247 Ų buried · 14 hydrogen bonds · protein-protein
- C–F · 1219 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1208 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 615 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 615 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 3M2P · The crystal structure of UDP-N-acetylglucosamine 4-epimerase from Bacillus cereus · 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 Q814Z6
- Elsewhere: RCSB PDB 3M2P · PDBe 3M2P · UniProt Q814Z6
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