MolNFT v1 · #48608 · protein
Azotobacter vinelandii mannuronan C-5 epimerase ALGE4 a-module complexed with mannuronan trisaccharide
2PYH · POLY(BETA-D-mannuronate) C5 epimerase 4: “Azotobacter vinelandii mannuronan C-5 epimerase ALGE4 a-module complexed with mannuronan trisaccharide”. X-ray diffraction, 2 ligands (MAV, CA), 3 pockets (best druggability 0.35). MolNFT v1…
- PDB
- 2PYH
- Type
- protein
- Length
- 753 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- POLY(BETA-D-mannuronate) C5 epimerase 4
- EC
- 5.1.3.-
- UniProt
- Q44493
- Ligands
- MAV, CA
- Pockets
- 3 · best druggability 0.35
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | POLY(BETA-D-mannuronate) C5 epimerase 4 (EC 5.1.3.-) | protein | 376 | 5% helix, 50% strand | Q44493 |
| B | POLY(BETA-D-mannuronate) C5 epimerase 4 (EC 5.1.3.-) | protein | 377 | 6% helix, 46% strand | Q44493 |
Ligands and binding sites
- MAV · alpha-D-mannopyranuronic acid · ligand · 3 copies · chains B
- CA · Calcium ion · metal · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.35 | 0.73 | 23 | MAV |
| 2 | 91 | 0.35 | 0.75 | 23 | empty |
| 3 | 57 | 0.27 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 610 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2PYH · Azotobacter vinelandii Mannuronan C-5 epimerase AlgE4 A-module complexed with mannuronan… · the same entry in another collection · chain A against A, TM-score 1.00
- Q44493 · AlphaFold monomer V2.0 prediction for mannuronan C5-epimerase ALGE4 (Q44493) · 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 Q44493
- Elsewhere: RCSB PDB 2PYH · PDBe 2PYH · UniProt Q44493
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