Research workbench
Structure of the human replication protein a (rpa) trimerization core
Analyse Structure of the human replication protein a (rpa) trimerization core in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1L1O
- Type
- protein
- Length
- 820 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replication protein a 14 kda subunit; Replication protein a 32 kda subunit; Replication…
- UniProt
- P35244, P15927, P27694
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Replication protein a 14 kda subunit | protein | 115 | 17% helix, 36% strand | P35244 |
| B, E | Replication protein a 32 kda subunit | protein | 123 | 19% helix, 43% strand | P15927 |
| C | Replication protein a 70 kda DNA-binding subunit | protein | 173 | 28% helix, 36% strand | P27694 |
| F | Replication protein a 70 kda DNA-binding subunit | protein | 171 | 29% helix, 36% strand | P27694 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 378 | 0.71 | 0.83 | 49 | empty |
| 2 | 167 | 0.69 | 0.88 | 30 | empty |
| 3 | 311 | 0.58 | 0.77 | 24 | empty |
| 4 | 170 | 0.52 | 0.79 | 18 | empty |
| 5 | 110 | 0.43 | 0.77 | 23 | empty |
Interfaces
10 interfaces between chains.
- D–E · 1330 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1234 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 964 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 961 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 418 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1L1O · Structure of the human Replication Protein A (RPA) trimerization core · the same entry in another collection · chain F against F, TM-score 1.00
- P35244 · AlphaFold monomer V2.0 prediction for replication protein a 14 kda subunit (P35244) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P15927 · AlphaFold monomer V2.0 prediction for replication protein a 32 kda subunit (P15927) · a predicted model of the same protein · chain B against A, TM-score 0.97
- P27694 · AlphaFold monomer V2.0 prediction for replication protein a 70 kda DNA-binding subunit… · a predicted model of the same protein · chain F against A, TM-score 0.97
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 P35244
- Every structure of UniProt P15927
- Every structure of UniProt P27694
- Elsewhere: RCSB PDB 1L1O · PDBe 1L1O · UniProt P35244 · UniProt P15927 · UniProt P27694
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