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Crystal structure of udp-glcnac 2-epimerase
Analyse Crystal structure of udp-glcnac 2-epimerase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZHT
- Type
- protein
- Length
- 1,532 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional udp-N-acetylglucosamine 2-EPIMERASE/N- acetylmannosamine kinase
- EC
- 3.2.1.183
- UniProt
- Q9Y223
- Ligands
- UDP, NCC, BM7
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional udp-N-acetylglucosamine 2-EPIMERASE/N- acetylmannosamine kinase (EC 3.2.1.183) | protein | 384 | 45% helix, 16% strand | Q9Y223 |
| B | Bifunctional udp-N-acetylglucosamine 2-EPIMERASE/N- acetylmannosamine kinase (EC 3.2.1.183) | protein | 382 | 46% helix, 16% strand | Q9Y223 |
| C | Bifunctional udp-N-acetylglucosamine 2-EPIMERASE/N- acetylmannosamine kinase (EC 3.2.1.183) | protein | 383 | 45% helix, 16% strand | Q9Y223 |
| D | Bifunctional udp-N-acetylglucosamine 2-EPIMERASE/N- acetylmannosamine kinase (EC 3.2.1.183) | protein | 383 | 45% helix, 16% strand | Q9Y223 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- NCC · Cytidine-5'-monophosphate-5-N-acetylneuraminic acid · ligand · 4 copies · chains A, B, C, D
- BM7 · 2-acetamido-2-deoxy-beta-D-mannopyranose · ligand · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 325 | 0.82 | 0.92 | 64 | UDP, BM7 |
| 2 | 313 | 0.81 | 0.92 | 64 | UDP |
| 3 | 267 | 0.79 | 0.91 | 50 | UDP |
| 4 | 256 | 0.79 | 0.91 | 49 | UDP |
| 5 | 62 | 0.70 | 0.96 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1891 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1842 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 413 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified (engineered).
Compared structures
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 Q9Y223
- Elsewhere: RCSB PDB 4ZHT · PDBe 4ZHT · UniProt Q9Y223
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