Research workbench
Crystal structure of MOEO5 soaked with 3-phosphoglycerate
Analyse Crystal structure of MOEO5 soaked with 3-phosphoglycerate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VKD
- Type
- protein
- Length
- 505 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MOEO5
- UniProt
- A0A011
- Ligands
- FPQ, MG, PO4
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MOEO5 | protein | 253 | 41% helix, 19% strand | A0A011 |
| B | MOEO5 | protein | 252 | 41% helix, 19% strand | A0A011 |
Ligands and binding sites
- FPQ · (2R)-3-(phosphonooxy)-2-{[(2Z,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]oxy}propanoic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 312 | 0.74 | 0.86 | 33 | PO4, FPQ |
| 2 | 319 | 0.74 | 0.86 | 36 | FPQ |
| 3 | 136 | 0.55 | 0.82 | 22 | empty |
| 4 | 109 | 0.47 | 0.80 | 22 | empty |
| 5 | 81 | 0.41 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1186 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3VKD · Crystal structure of MoeO5 soaked with 3-phosphoglycerate · the same entry in another collection · chain B against B, 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 A0A011
- Elsewhere: RCSB PDB 3VKD · PDBe 3VKD · UniProt A0A011
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