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Crystal structure of transcriptional regulator NMB0573 from neisseria meningitidis
Analyse Crystal structure of transcriptional regulator NMB0573 from neisseria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P5V
- Type
- protein
- Length
- 1,244 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator, LRP/ASNC family
- UniProt
- Q9K0L9
- Ligands
- CA, CL
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Transcriptional regulator, LRP/ASNC family | protein | 156 | 38% helix, 29% strand | Q9K0L9 |
| C, F, H | Transcriptional regulator, LRP/ASNC family | protein | 154 | 38% helix, 30% strand | Q9K0L9 |
| G | Transcriptional regulator, LRP/ASNC family | protein | 158 | 41% helix, 29% strand | Q9K0L9 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, G, B, D, C, E, F, H
- CL · Chloride ion · ion · 10 copies · chains A, D, B, G, C, F, E, H
- GOL · Glycerol · additive · 8 copies · chains A, D, B, G, C, E, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.76 | 0.86 | 71 | GOL |
| 2 | 265 | 0.73 | 0.87 | 45 | GOL |
| 3 | 246 | 0.72 | 0.87 | 45 | GOL |
| 4 | 389 | 0.72 | 0.83 | 53 | GOL |
| 5 | 353 | 0.72 | 0.84 | 52 | GOL |
Interfaces
16 interfaces between chains.
- C–D · 3389 Ų buried · 68 hydrogen bonds · protein-protein
- G–H · 3375 Ų buried · 68 hydrogen bonds · protein-protein
- A–B · 3350 Ų buried · 68 hydrogen bonds · protein-protein
- E–F · 3287 Ų buried · 61 hydrogen bonds · protein-protein
- C–F · 484 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 2P5V · Crystal Structure of Transcriptional Regulator NMB0573 from Neisseria Meningitidis · 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 Q9K0L9
- Elsewhere: RCSB PDB 2P5V · PDBe 2P5V · UniProt Q9K0L9
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