Research workbench
Human C3PO complex in the presence of MNSO4
Analyse Human C3PO complex in the presence of MNSO4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QB5
- Type
- protein
- Length
- 861 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Translin; Translin-associated protein X
- UniProt
- Q15631, Q99598
- Ligands
- NA, MN, PO4, SO4, CL
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Translin | protein | 213 | 78% helix, 0% strand | Q15631 |
| B | Translin | protein | 218 | 74% helix, 0% strand | Q15631 |
| C | Translin | protein | 208 | 73% helix, 0% strand | Q15631 |
| K | Translin-associated protein X | protein | 222 | 76% helix, 2% strand | Q99598 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- MN · Manganese (II) ion · metal · chains C, K
- PO4 · Phosphate ion · ion · 2 copies · chains C, K
- SO4 · Sulfate ion · ion · 2 copies · chains C, K
- CL · Chloride ion · ion · chains A, C, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 586 | 0.74 | 0.81 | 48 | empty |
| 2 | 504 | 0.74 | 0.82 | 37 | empty |
| 3 | 357 | 0.67 | 0.81 | 32 | empty |
| 4 | 434 | 0.66 | 0.79 | 41 | empty |
| 5 | 71 | 0.49 | 0.84 | 16 | empty |
Interfaces
6 interfaces between chains.
- C–K · 1279 Ų buried · 12 hydrogen bonds · protein-protein
- B–K · 989 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 788 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 751 Ų buried · 14 hydrogen bonds · protein-protein
- A–K · 173 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3QB5 · Human C3PO complex in the presence of MnSO4 · the same entry in another collection · chain K against K, TM-score 1.00
- Q15631 · AlphaFold monomer V2.0 prediction for translin (Q15631) · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q99598 · AlphaFold monomer V2.0 prediction for translin-associated protein X (Q99598) · a predicted model of the same protein · chain K against A, TM-score 0.96
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 Q15631
- Every structure of UniProt Q99598
- Elsewhere: RCSB PDB 3QB5 · PDBe 3QB5 · UniProt Q15631 · UniProt Q99598
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