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The structural basis for the internal interaction in RBBP5
Analyse The structural basis for the internal interaction in RBBP5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KM7
- Type
- protein
- Length
- 691 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoblastoma-binding protein 5
- UniProt
- Q15291
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 2% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoblastoma-binding protein 5 | protein | 313 | 2% helix, 53% strand | Q15291 |
| B | Retinoblastoma-binding protein 5 | protein | 312 | 2% helix, 53% strand | Q15291 |
| C | Retinoblastoma-binding protein 5 | protein | 32 | 0% helix, 13% strand | Q15291 |
| D | Retinoblastoma-binding protein 5 | protein | 34 | 0% helix, 9% strand | Q15291 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, D
- 2PE · Nonaethylene glycol · additive · chains A, C
- P6G · Hexaethylene glycol · additive · chains B
- PG4 · Tetraethylene glycol · additive · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 866 | 0.83 | 0.85 | 70 | SO4 |
| 2 | 1107 | 0.83 | 0.84 | 85 | SO4, PG4 |
| 3 | 143 | 0.55 | 0.82 | 26 | empty |
| 4 | 172 | 0.46 | 0.76 | 24 | SO4 |
| 5 | 68 | 0.39 | 0.79 | 13 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1467 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1382 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 381 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 184 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 151 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6KM7 · The structural basis for the internal interaction in RBBP5 · the same entry in another collection · chain D against D, TM-score 1.00
- Q15291 · AlphaFold monomer V2.0 prediction for retinoblastoma-binding protein 5 (Q15291) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q15291
- Elsewhere: RCSB PDB 6KM7 · PDBe 6KM7 · UniProt Q15291
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