MolNFT v1 · #58930 · protein
Crystal structure of the NMB1088 protein from neisseria meningitidis. northeast structural genomics consortium target MR91
3BID · UPF0339 protein NMB1088: “Crystal structure of the NMB1088 protein from neisseria meningitidis. northeast structural genomics…”. X-ray diffraction, 1 pocket (best druggability 0.26). MolNFT v1 #58930 on GenesisL1: 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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