MolNFT v1 · #126599 · protein
Crystal structure of ntrx from brucella abortus in complex with ADP processed with the crystaldirect automated mounting and cryo-cooling technology
5M7P · Nitrogen assimilation regulatory protein: “Crystal structure of ntrx from brucella abortus in complex with ADP processed with the crystaldirect…”. X-ray diffraction, 2 ligands (ADP, MG), 9 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 5M7P
- Type
- protein
- Length
- 878 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrogen assimilation regulatory protein
- UniProt
- C4IRH0
- Ligands
- ADP, MG
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrogen assimilation regulatory protein | protein | 441 | 51% helix, 13% strand | C4IRH0 |
| B | Nitrogen assimilation regulatory protein | protein | 437 | 53% helix, 14% strand | C4IRH0 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1059 | 0.85 | 0.86 | 118 | ADP |
| 2 | 589 | 0.71 | 0.79 | 72 | empty |
| 3 | 204 | 0.59 | 0.81 | 30 | empty |
| 4 | 112 | 0.55 | 0.84 | 17 | empty |
| 5 | 76 | 0.50 | 0.84 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 4833 Ų buried · 68 hydrogen bonds · protein-protein
Compared structures
- 5M7P · Crystal structure of NtrX from Brucella abortus in complex with ADP processed with the… · the same entry in another collection · chain A against A, TM-score 1.00
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 C4IRH0
- Elsewhere: RCSB PDB 5M7P · PDBe 5M7P · UniProt C4IRH0
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