MolNFT v1 · #47717 · protein
Crystal structure of transcriptional regulator NMB0573 and L-leucine complex from neisseria meningitidis
2P6T · Transcriptional regulator, LRP/ASNC family: “Crystal structure of transcriptional regulator NMB0573 and L-leucine complex from neisseria meningitidis”. X-ray diffraction, 2 ligands (LEU, CA), 20 pockets (best druggability 0.84).…
- PDB
- 2P6T
- 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
- LEU, CA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 38% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Transcriptional regulator, LRP/ASNC family | protein | 156 | 39% helix, 29% strand | Q9K0L9 |
| B | Transcriptional regulator, LRP/ASNC family | protein | 157 | 38% helix, 29% strand | Q9K0L9 |
| C, E, H | Transcriptional regulator, LRP/ASNC family | protein | 154 | 41% helix, 30% strand | Q9K0L9 |
| F | Transcriptional regulator, LRP/ASNC family | protein | 155 | 37% helix, 30% strand | Q9K0L9 |
| G | Transcriptional regulator, LRP/ASNC family | protein | 158 | 34% helix, 29% strand | Q9K0L9 |
Ligands and binding sites
- LEU · Leucine · ligand · 8 copies · chains A, B, G, D, C, F, E, H
- CA · Calcium ion · metal · 11 copies · chains B, G, D, C, F, E, A, H
- GOL · Glycerol · additive · 6 copies · chains A, C, F, D, E, 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 956 | 0.84 | 0.86 | 117 | CA |
| 2 | 142 | 0.74 | 0.93 | 32 | empty |
| 3 | 275 | 0.74 | 0.87 | 43 | CA |
| 4 | 161 | 0.73 | 0.91 | 31 | empty |
| 5 | 520 | 0.72 | 0.81 | 72 | CA, GOL |
Interfaces
19 interfaces between chains.
- E–F · 3366 Ų buried · 64 hydrogen bonds · protein-protein
- A–B · 3351 Ų buried · 57 hydrogen bonds · protein-protein
- G–H · 3335 Ų buried · 64 hydrogen bonds · protein-protein
- C–D · 3258 Ų buried · 63 hydrogen bonds · protein-protein
- B–G · 480 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 2P6T · CRYSTAL STRUCTURE OF TRANSCRIPTIONAL REGULATOR NMB0573 and L-LEUCINE COMPLEX FROM… · the same entry in another collection · chain G against G, 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 2P6T · PDBe 2P6T · UniProt Q9K0L9
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