Research workbench
Crystal structure of nolr from sinorhizobium fredii
Analyse Crystal structure of nolr from sinorhizobium fredii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OMZ
- Type
- protein
- Length
- 785 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nolr
- UniProt
- Q83TD2
- Ligands
- PO4
- Pockets
- 12 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 64% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Nolr | protein | 98 | 64% helix, 12% strand | Q83TD2 |
| B, D, E, G | Nolr | protein | 98 | 63% helix, 12% strand | Q83TD2 |
| C | Nolr | protein | 100 | 63% helix, 12% strand | Q83TD2 |
| H | Nolr | protein | 97 | 66% helix, 12% strand | Q83TD2 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 14 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 658 | 0.70 | 0.78 | 77 | empty |
| 2 | 233 | 0.60 | 0.80 | 25 | empty |
| 3 | 197 | 0.56 | 0.80 | 25 | empty |
| 4 | 104 | 0.56 | 0.84 | 14 | empty |
| 5 | 167 | 0.56 | 0.80 | 17 | empty |
Interfaces
14 interfaces between chains.
- E–F · 1548 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 1515 Ų buried · 6 hydrogen bonds · protein-protein
- G–H · 1494 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1475 Ų buried · 5 hydrogen bonds · protein-protein
- F–H · 513 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4OMZ · Crystal Structure of NolR from Sinorhizobium fredii · 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 Q83TD2
- Elsewhere: RCSB PDB 4OMZ · PDBe 4OMZ · UniProt Q83TD2
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