Research workbench
Crystal structure of a dimer of N-terminal domains of ahrc in complex with an 18BP DNA operator site
Analyse Crystal structure of a dimer of N-terminal domains of ahrc in complex with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P5L
- Type
- protein + DNA
- Length
- 325 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*DCP*DAP*DTP*DGP*DAP*DAP*DTP*DAP*DAP*DAP*DAP*DAP*DTP*DTP*DCP*DAP*DA P*DG)-3')…
- UniProt
- P17893
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | DNA (5'- D(*DCP*DAP*DTP*DGP*DAP*DAP*DTP*DAP*DAP*DAP*DAP*DAP*DTP*DTP*DCP*DAP*DA P*DG)-3') | dna | 18 | — | — |
| B | DNA (5'- D(*DCP*DTP*DTP*DGP*DAP*DAP*DTP*DTP*DTP*DTP*DTP*DAP*DTP*DTP*DCP*DAP*DT P*DG)-3') | dna | 18 | — | — |
| F | DNA (5'- D(*DCP*DTP*DTP*DGP*DAP*DAP*DTP*DTP*DTP*DTP*DTP*DAP*DTP*DTP*DCP*DAP*DT P*DG)-3') | dna | 17 | — | — |
| C, G | Arginine repressor | protein | 63 | 54% helix, 13% strand | P17893 |
| D, H | Arginine repressor | protein | 64 | 55% helix, 13% strand | P17893 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains D, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.73 | 0.97 | 24 | empty |
| 2 | 173 | 0.71 | 0.90 | 27 | empty |
| 3 | 79 | 0.40 | 0.78 | 15 | empty |
| 4 | 75 | 0.32 | 0.75 | 19 | empty |
| 5 | 55 | 0.31 | 0.76 | 14 | empty |
Interfaces
18 interfaces between chains.
- A–B · 835 Ų buried · 78 hydrogen bonds · nucleic-nucleic
- E–F · 793 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- C–D · 523 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 433 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–C · 395 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 2P5L · Crystal structure of a dimer of N-terminal domains of AhrC in complex with an 18bp DNA… · the same entry in another collection · chain H against H, TM-score 1.00
- P17893 · AlphaFold monomer V2.0 prediction for arginine repressor (P17893) · a predicted model of the same protein · chain H 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 P17893
- Elsewhere: RCSB PDB 2P5L · PDBe 2P5L · UniProt P17893
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