Research workbench
Crystal structure of the NMB1088 protein from neisseria meningitidis. northeast structural genomics consortium target MR91
Analyse Crystal structure of the NMB1088 protein from neisseria meningitidis. northeast… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BID
- Type
- protein
- Length
- 466 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UPF0339 protein NMB1088
- UniProt
- Q7DDI1
- Pockets
- 1 · best druggability 0.26
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F | UPF0339 protein NMB1088 | protein | 58 | 21% helix, 34% strand | Q7DDI1 |
| B, D, H | UPF0339 protein NMB1088 | protein | 57 | 21% helix, 35% strand | Q7DDI1 |
| E | UPF0339 protein NMB1088 | protein | 61 | 20% helix, 34% strand | Q7DDI1 |
| G | UPF0339 protein NMB1088 | protein | 60 | 20% helix, 33% strand | Q7DDI1 |
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.26 | 0.72 | 13 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1564 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1556 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 1485 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1441 Ų buried · 18 hydrogen bonds · protein-protein
- B–H · 298 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3BID · Crystal structure of the NMB1088 protein from Neisseria meningitidis. Northeast… · the same entry in another collection · chain H against H, TM-score 1.00
- Q7DDI1 · AlphaFold monomer V2.0 prediction for UPF0339 protein NMB1088 (Q7DDI1) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q7DDI1
- Elsewhere: RCSB PDB 3BID · PDBe 3BID · UniProt Q7DDI1
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