Research workbench
Crystal structure of RPA70N in complex with a 3,4 dichlorophenylalanine atrip derived peptide
Analyse Crystal structure of RPA70N in complex with a 3,4 dichlorophenylalanine atrip… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NB3
- Type
- protein
- Length
- 271 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replication protein a 70 kda DNA-binding subunit; 3,4 dichlorophenylalanine atrip derived…
- UniProt
- P27694
- Ligands
- 2N2
- Pockets
- 1 · best druggability 0.45
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replication protein a 70 kda DNA-binding subunit | protein | 123 | 19% helix, 39% strand | P27694 |
| B | Replication protein a 70 kda DNA-binding subunit | protein | 122 | 19% helix, 39% strand | P27694 |
| C, D | 3,4 dichlorophenylalanine atrip derived peptide | protein | 13 | 54% helix, 0% strand | — |
Ligands and binding sites
- 2N2 · 2-(3,6-dihydroxy-9H-xanthen-9-yl)-5-{[(6-oxohexyl) carbamothioyl]amino}benzoic acid · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.45 | 0.81 | 22 | empty |
Interfaces
4 interfaces between chains.
- B–D · 642 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 633 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 547 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 23 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 4NB3 · Crystal structure of RPA70N in complex with a 3,4 dichlorophenylalanine ATRIP derived… · the same entry in another collection · chain A against A, TM-score 1.00
- P27694 · AlphaFold monomer V2.0 prediction for replication protein a 70 kda DNA-binding subunit… · a predicted model of the same protein · chain B against A, TM-score 0.93
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 P27694
- Elsewhere: RCSB PDB 4NB3 · PDBe 4NB3 · UniProt P27694
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