MolNFT v1 · #56382 · protein
Crystal structure of prefoldin from pyrococcus horikoshii OT3
2ZDI · Prefoldin subunit beta: “Crystal structure of prefoldin from pyrococcus horikoshii OT3”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.42). MolNFT v1 #56382 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2ZDI
- Type
- protein
- Length
- 355 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prefoldin subunit beta; Prefoldin subunit alpha
- UniProt
- O58268, O58263
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.42
Structure
x-ray diffraction · 3 distinct chains · 68% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prefoldin subunit beta | protein | 101 | 74% helix, 10% strand | O58268 |
| B | Prefoldin subunit beta | protein | 106 | 77% helix, 11% strand | O58268 |
| C | Prefoldin subunit alpha | protein | 148 | 56% helix, 16% strand | O58263 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.42 | 0.73 | 28 | empty |
| 2 | 132 | 0.38 | 0.73 | 20 | empty |
Interfaces
2 interfaces between chains.
- B–C · 657 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 588 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2ZDI · Crystal structure of Prefoldin from Pyrococcus horikoshii OT3 · the same entry in another collection · chain A against A, TM-score 1.00
- O58268 · AlphaFold monomer V2.0 prediction for prefoldin subunit beta (O58268) · a predicted model of the same protein · chain B against A, TM-score 0.94
- O58263 · AlphaFold monomer V2.0 prediction for prefoldin subunit alpha (O58263) · a predicted model of the same protein · chain C against A, TM-score 0.93
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 O58268
- Every structure of UniProt O58263
- Elsewhere: RCSB PDB 2ZDI · PDBe 2ZDI · UniProt O58268 · UniProt O58263
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