Research workbench
Crystal structure of S. cerevisiae RFA1 N-ob domain mutant (K45E)
Analyse Crystal structure of S. cerevisiae RFA1 N-ob domain mutant (K45E) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M1X
- Type
- protein
- Length
- 518 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replication factor a protein 1
- UniProt
- P22336
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replication factor a protein 1 | protein | 130 | 22% helix, 37% strand | P22336 |
| B | Replication factor a protein 1 | protein | 127 | 22% helix, 34% strand | P22336 |
| C | Replication factor a protein 1 | protein | 128 | 25% helix, 36% strand | P22336 |
| D | Replication factor a protein 1 | protein | 133 | 23% helix, 36% strand | P22336 |
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 | 598 | 0.73 | 0.80 | 84 | empty |
| 2 | 173 | 0.53 | 0.79 | 23 | empty |
| 3 | 175 | 0.52 | 0.79 | 25 | empty |
| 4 | 132 | 0.43 | 0.76 | 24 | empty |
| 5 | 133 | 0.43 | 0.76 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–C · 632 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 529 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 250 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 207 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 27 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 5M1X · Crystal structure of S. cerevisiae Rfa1 N-OB domain mutant (K45E) · the same entry in another collection · chain D against D, 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 0.94
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 P22336
- Elsewhere: RCSB PDB 5M1X · PDBe 5M1X · UniProt P22336
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