Research workbench
Crystal structure of transcriptional regulator NMB0573/L-met complex from neisseria meningitidis
Analyse Crystal structure of transcriptional regulator NMB0573/L-met complex from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P6S
- 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
- MET, CA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 37% 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 | 37% helix, 29% strand | Q9K0L9 |
| G | Transcriptional regulator, LRP/ASNC family | protein | 158 | 35% helix, 29% strand | Q9K0L9 |
Ligands and binding sites
- MET · Methionine · ligand · 8 copies · chains A, B, G, D, C, F, E, H
- CA · Calcium ion · metal · 9 copies · chains B, H, G, C, F, A, D, E
- GOL · Glycerol · additive · 12 copies · chains A, D, C, B, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1091 | 0.85 | 0.86 | 129 | CA, MET |
| 2 | 827 | 0.81 | 0.84 | 85 | MET, GOL |
| 3 | 155 | 0.74 | 0.92 | 30 | empty |
| 4 | 262 | 0.72 | 0.86 | 47 | CA |
| 5 | 447 | 0.71 | 0.82 | 62 | CA |
Interfaces
20 interfaces between chains.
- E–F · 3360 Ų buried · 65 hydrogen bonds · protein-protein
- A–B · 3352 Ų buried · 61 hydrogen bonds · protein-protein
- C–D · 3306 Ų buried · 60 hydrogen bonds · protein-protein
- G–H · 3278 Ų buried · 68 hydrogen bonds · protein-protein
- A–D · 488 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 2P6S · Crystal Structure of Transcriptional Regulator NMB0573/L-Met Complex from Neisseria… · 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 2P6S · PDBe 2P6S · UniProt Q9K0L9
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