Research workbench
Yeast RPA bound to ssDNA
Analyse Yeast RPA bound to ssDNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I52
- Type
- protein + DNA
- Length
- 452 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.7
- Source
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c); SYNTHETIC CONSTRUCT
- Molecule
- Replication factor A protein 3; Replication factor A protein 2; Replication factor A…
- UniProt
- P26755, P26754, P22336
- Pockets
- 15 · best druggability 0.76
Structure
electron microscopy · resolution 4.7 · 4 distinct chains · 19% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replication factor A protein 3 | protein | 122 | 14% helix, 30% strand | P26755 |
| B | Replication factor A protein 2 | protein | 132 | 17% helix, 24% strand | P26754 |
| C | Replication factor A protein 1 | protein | 178 | 23% helix, 29% strand | P22336 |
| D | DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') | dna | 20 | — | — |
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 654 | 0.76 | 0.82 | 65 | empty |
| 2 | 54 | 0.67 | 0.96 | 23 | empty |
| 3 | 299 | 0.65 | 0.81 | 33 | empty |
| 4 | 309 | 0.62 | 0.79 | 34 | empty |
| 5 | 268 | 0.59 | 0.79 | 41 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1239 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–B · 1061 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 926 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 599 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–C · 394 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6I52 · Yeast rpa bound to ssdna · the same entry in another collection · chain A against A, TM-score 1.00
- P22336 · AlphaFold monomer V2.0 prediction for replication factor a protein 1 (P22336) · a predicted model of the same protein · chain C against A, TM-score 0.89
- P26754 · AlphaFold monomer V2.0 prediction for replication factor a protein 2 (P26754) · a predicted model of the same protein · chain B against A, TM-score 0.82
- P26755 · AlphaFold monomer V2.0 prediction for replication factor a protein 3 (P26755) · a predicted model of the same protein · chain A against A, TM-score 0.76
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 P26755
- Every structure of UniProt P26754
- Every structure of UniProt P22336
- Elsewhere: RCSB PDB 6I52 · PDBe 6I52 · UniProt P26755 · UniProt P26754 · UniProt P22336
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