MolNFT v1 · #141806 · protein
Structure of N-acetylmannosamine-6-phosphate-2-epimerase from vibrio cholerae with N-acetylglucosamine-6-phosphate
5ZJP · Putative N-acetylmannosamine-6-phosphate 2-epimerase: “Structure of N-acetylmannosamine-6-phosphate-2-epimerase from vibrio cholerae with…”. X-ray diffraction, 1 ligand (RFW), 4 pockets (best druggability 0.73). MolNFT v1 #141806 on…
- PDB
- 5ZJP
- Type
- protein
- Length
- 453 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative N-acetylmannosamine-6-phosphate 2-epimerase
- EC
- 5.1.3.9
- UniProt
- A0A2K2UT85
- Ligands
- RFW
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative N-acetylmannosamine-6-phosphate 2-epimerase (EC 5.1.3.9) | protein | 223 | 43% helix, 17% strand | A0A2K2UT85 |
| B | Putative N-acetylmannosamine-6-phosphate 2-epimerase (EC 5.1.3.9) | protein | 230 | 42% helix, 16% strand | A0A2K2UT85 |
Ligands and binding sites
- RFW · N-acetyl-D-glucosamine-6-phosphate · ligand · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B
- PGE · Triethylene glycol · additive · chains A, B
- EDO · 1,2-ethanediol · additive · chains 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 | 58 | 0.73 | 0.98 | 21 | empty |
| 2 | 233 | 0.63 | 0.82 | 30 | RFW |
| 3 | 214 | 0.59 | 0.80 | 26 | RFW |
| 4 | 124 | 0.48 | 0.78 | 18 | PGE |
Interfaces
1 interface between chains.
- A–B · 1756 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5ZJP · Structure of N-acetylmannosamine-6-phosphate-2-epimerase from Vibrio cholerae with… · 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 A0A2K2UT85
- Elsewhere: RCSB PDB 5ZJP · PDBe 5ZJP · UniProt A0A2K2UT85
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