Research workbench
Crystal structure of lipoprotein GNA1946 from neisseria meningitidis
Analyse Crystal structure of lipoprotein GNA1946 from neisseria meningitidis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IR1
- Type
- protein
- Length
- 1,444 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane lipoprotein GNA1946
- UniProt
- Q7BMQ8
- Ligands
- MET, SO4
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E | Outer membrane lipoprotein GNA1946 | protein | 239 | 40% helix, 24% strand | Q7BMQ8 |
| B, F | Outer membrane lipoprotein GNA1946 | protein | 244 | 40% helix, 23% strand | Q7BMQ8 |
Ligands and binding sites
- MET · Methionine · ligand · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 18 copies · chains A, B, C, E, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.81 | 0.82 | 90 | SO4 |
| 2 | 1062 | 0.80 | 0.81 | 96 | empty |
| 3 | 53 | 0.71 | 0.98 | 25 | MET |
| 4 | 50 | 0.70 | 0.98 | 23 | MET |
| 5 | 345 | 0.58 | 0.76 | 48 | SO4 |
Interfaces
8 interfaces between chains.
- D–E · 724 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 662 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 487 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 479 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 466 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3IR1 · Crystal Structure of Lipoprotein GNA1946 from Neisseria meningitidis · the same entry in another collection · chain B against B, 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 Q7BMQ8
- Elsewhere: RCSB PDB 3IR1 · PDBe 3IR1 · UniProt Q7BMQ8
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