MolNFT v1 · #183054 · protein
Crystal structure of nanobody NB_MSBA#1 in complex with the nucleotide binding domain of msba
7NDF · NB_MSBA 1: “Crystal structure of nanobody NB_MSBA#1 in complex with the nucleotide binding domain of msba”. X-ray diffraction, 7 pockets (best druggability 0.85). MolNFT v1 #183054 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7NDF
- Type
- protein
- Length
- 707 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NB_MSBA 1; Lipid a ABC transporter ATP-binding PROTEIN/PERMEASE msba
- UniProt
- A0A786F4A3
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | NB_MSBA 1 | protein | 113 | 3% helix, 50% strand | — |
| A | Lipid a ABC transporter ATP-binding PROTEIN/PERMEASE msba | protein | 241 | 37% helix, 24% strand | A0A786F4A3 |
| B | Lipid a ABC transporter ATP-binding PROTEIN/PERMEASE msba | protein | 240 | 35% helix, 25% strand | A0A786F4A3 |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 653 | 0.85 | 0.90 | 110 | empty |
| 2 | 117 | 0.56 | 0.84 | 20 | empty |
| 3 | 102 | 0.55 | 0.84 | 20 | empty |
| 4 | 75 | 0.49 | 0.83 | 20 | empty |
| 5 | 98 | 0.42 | 0.77 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2116 Ų buried · 31 hydrogen bonds · protein-protein
- D–A · 800 Ų buried · 17 hydrogen bonds · protein-protein
- C–B · 771 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7NDF · Crystal structure of nanobody Nb_MsbA#1 in complex with the nucleotide binding domain of… · the same entry in another collection · chain C against C, 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 A0A786F4A3
- Elsewhere: RCSB PDB 7NDF · PDBe 7NDF · UniProt A0A786F4A3
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