MolNFT v1 · #26774 · protein
Crystal structure of pyrococcus horikoshii mannosyl-3-phosphoglycerate phosphatase complexed with MG2+ and phosphate
1WZC: “Crystal structure of pyrococcus horikoshii mannosyl-3-phosphoglycerate phosphatase complexed with MG2+ and…”. X-ray diffraction, 2 ligands (MG, PO4), 5 pockets (best druggability 0.77). MolNFT v1 #26774 on GenesisL1: 3D structure…
- PDB
- 1WZC
- Type
- protein
- Length
- 478 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannosyl-3-phosphoglycerate phosphatase
- EC
- 3.1.3.70
- UniProt
- O58690
- Ligands
- MG, PO4
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mannosyl-3-phosphoglycerate phosphatase (EC 3.1.3.70) | protein | 234 | 39% helix, 23% strand | O58690 |
| B | Mannosyl-3-phosphoglycerate phosphatase (EC 3.1.3.70) | protein | 244 | 36% helix, 24% strand | O58690 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.77 | 0.98 | 23 | PO4 |
| 2 | 85 | 0.75 | 0.98 | 21 | PO4 |
| 3 | 207 | 0.53 | 0.78 | 26 | empty |
| 4 | 126 | 0.49 | 0.79 | 22 | empty |
| 5 | 58 | 0.36 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 320 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1WZC · Crystal structure of Pyrococcus horikoshii mannosyl-3-phosphoglycerate phosphatase… · the same entry in another collection · chain A against A, TM-score 1.00
- O58690 · AlphaFold monomer V2.0 prediction for mannosyl-3-phosphoglycerate phosphatase (O58690) · a predicted model of the same protein · chain B 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 O58690
- Elsewhere: RCSB PDB 1WZC · PDBe 1WZC · UniProt O58690
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