Research workbench
Structure of the SHQ1P-CBF5P complex
Analyse Structure of the SHQ1P-CBF5P complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZV0
- Type
- protein
- Length
- 963 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein SHQ1; H/ACA ribonucleoprotein complex subunit 4
- EC
- 5.4.99.-
- UniProt
- P40486, P33322
- Pockets
- 14 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein SHQ1 | protein | 325 | 63% helix, 5% strand | P40486 |
| B | Protein SHQ1 | protein | 329 | 62% helix, 5% strand | P40486 |
| C | H/ACA ribonucleoprotein complex subunit 4 (EC 5.4.99.-) | protein | 152 | 28% helix, 24% strand | P33322 |
| D | H/ACA ribonucleoprotein complex subunit 4 (EC 5.4.99.-) | protein | 157 | 27% helix, 24% strand | P33322 |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.72 | 0.92 | 19 | GOL |
| 2 | 434 | 0.70 | 0.81 | 56 | empty |
| 3 | 371 | 0.68 | 0.81 | 40 | empty |
| 4 | 234 | 0.49 | 0.75 | 28 | empty |
| 5 | 182 | 0.47 | 0.76 | 25 | empty |
Interfaces
5 interfaces between chains.
- C–D · 3226 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 2104 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 2081 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 199 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 197 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3ZV0 · Structure of the SHQ1P-CBF5P complex · the same entry in another collection · chain D against D, TM-score 1.00
- P40486 · AlphaFold monomer V2.0 prediction for protein SHQ1 (P40486) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P33322 · AlphaFold monomer V2.0 prediction for H/ACA ribonucleoprotein complex subunit CBF5… · a predicted model of the same protein · chain C against A, TM-score 0.63
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 P40486
- Every structure of UniProt P33322
- Elsewhere: RCSB PDB 3ZV0 · PDBe 3ZV0 · UniProt P40486 · UniProt P33322
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