Research workbench
Human cohesin regulator PDS5B bound to a wapl peptide
Analyse Human cohesin regulator PDS5B bound to a wapl peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HDT
- Type
- protein
- Length
- 2,163 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sister chromatid cohesion protein PDS5 homolog B; Wings apart-like protein homolog
- UniProt
- Q9NTI5, Q7Z5K2
- Ligands
- IHP
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sister chromatid cohesion protein PDS5 homolog B | protein | 1085 | 73% helix, 0% strand | Q9NTI5 |
| B | Sister chromatid cohesion protein PDS5 homolog B | protein | 1073 | 72% helix, 0% strand | Q9NTI5 |
| E | Wings apart-like protein homolog | protein | 5 | 0% helix, 0% strand | Q7Z5K2 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 279 | 0.67 | 0.83 | 40 | empty |
| 2 | 765 | 0.67 | 0.75 | 56 | empty |
| 3 | 175 | 0.63 | 0.84 | 31 | empty |
| 4 | 377 | 0.61 | 0.77 | 40 | empty |
| 5 | 228 | 0.58 | 0.79 | 23 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1184 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 509 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 68 modified (engineered).
Compared structures
- 5HDT · Human cohesin regulator Pds5B bound to a Wapl peptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NTI5 · AlphaFold monomer V2.0 prediction for sister chromatid cohesion protein PDS5 homolog B… · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q7Z5K2 · AlphaFold monomer V2.0 prediction for wings apart-like protein homolog (Q7Z5K2) · a predicted model of the same protein · chain E against A, TM-score 0.68
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 Q9NTI5
- Every structure of UniProt Q7Z5K2
- Elsewhere: RCSB PDB 5HDT · PDBe 5HDT · UniProt Q9NTI5 · UniProt Q7Z5K2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.