MolNFT v1 · #70300 · protein
Crystal structure of nikr from helicobacter pylori with variable ni site coordination
3LGH · Nickel-responsive regulator: “Crystal structure of nikr from helicobacter pylori with variable ni site coordination”. X-ray diffraction, 2 ligands (NI, MG), 3 pockets (best druggability 0.78). MolNFT v1 #70300 on GenesisL1: 3D…
- PDB
- 3LGH
- Type
- protein
- Length
- 427 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nickel-responsive regulator
- UniProt
- O25896
- Ligands
- NI, MG
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nickel-responsive regulator | protein | 131 | 41% helix, 34% strand | O25896 |
| B | Nickel-responsive regulator | protein | 139 | 37% helix, 32% strand | O25896 |
| C | Nickel-responsive regulator | protein | 79 | 30% helix, 46% strand | O25896 |
| D | Nickel-responsive regulator | protein | 78 | 31% helix, 45% strand | O25896 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.78 | 0.81 | 81 | empty |
| 2 | 225 | 0.49 | 0.75 | 30 | empty |
| 3 | 56 | 0.42 | 0.81 | 12 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1882 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1072 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 900 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 49 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3LGH · Crystal structure of NikR from Helicobacter pylori with variable Ni site coordination · the same entry in another collection · chain D against D, TM-score 1.00
- O25896 · AlphaFold monomer V2.0 prediction for putative nickel-responsive regulator (O25896) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 3LGH · PDBe 3LGH · UniProt O25896
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