Research workbench
Crystal structure of H.PYLORI nikr in complex with DNA
Analyse Crystal structure of H.PYLORI nikr in complex with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MRJ
- Type
- protein + DNA
- Length
- 628 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nickel-responsive regulator; DNA (36-mer)
- UniProt
- O25896
- Ligands
- NI, MG
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nickel-responsive regulator | protein | 134 | 42% helix, 34% strand | O25896 |
| B, C | Nickel-responsive regulator | protein | 142 | 39% helix, 34% strand | O25896 |
| D | Nickel-responsive regulator | protein | 138 | 40% helix, 32% strand | O25896 |
| L | DNA (36-mer) | dna | 36 | — | — |
| M | DNA (36-mer) | dna | 36 | — | — |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 4 copies · chains A, D, B, C
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.73 | 0.99 | 19 | empty |
| 2 | 623 | 0.68 | 0.78 | 59 | empty |
| 3 | 221 | 0.66 | 0.84 | 32 | empty |
| 4 | 237 | 0.55 | 0.78 | 31 | empty |
| 5 | 103 | 0.50 | 0.82 | 24 | empty |
Interfaces
15 interfaces between chains.
- C–D · 3411 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 3189 Ų buried · 45 hydrogen bonds · protein-protein
- L–M · 1567 Ų buried · 140 hydrogen bonds · nucleic-nucleic
- A–D · 967 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 926 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6MRJ · Crystal structure of H.pylori NikR in complex with DNA · the same entry in another collection · chain M against M, TM-score 1.00
- O25896 · AlphaFold monomer V2.0 prediction for putative nickel-responsive regulator (O25896) · a predicted model of the same protein · chain B against A, TM-score 0.75
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 O25896
- Elsewhere: RCSB PDB 6MRJ · PDBe 6MRJ · UniProt O25896
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