MolNFT v1 · #145020 · protein
Crystal structure of the single chain variable fragment of the DH270.6 bnab in complex with the MAN9-V3 glycopeptide
6CBP: “Crystal structure of the single chain variable fragment of the DH270.6 bnab in complex with the MAN9-V3…”. X-ray diffraction, 3 ligands (MAN, NAG, BMA), 1 pocket (best druggability 0.30). MolNFT v1 #145020 on GenesisL1: 3D…
- PDB
- 6CBP
- Type
- protein
- Length
- 265 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MAN9-V3 glycopeptide; DH270.6 single chain variable fragment
- UniProt
- Q74448
- Ligands
- MAN, NAG, BMA
- Pockets
- 1 · best druggability 0.30
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | MAN9-V3 glycopeptide | protein | 30 | 0% helix, 33% strand | Q74448 |
| A | DH270.6 single chain variable fragment | protein | 235 | 5% helix, 49% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains P, A
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 66 | 0.30 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- P–A · 476 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6CBP · Crystal structure of the single chain variable fragment of the DH270.6 bnAb in complex… · the same entry in another collection · chain P against P, 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 Q74448
- Elsewhere: RCSB PDB 6CBP · PDBe 6CBP · UniProt Q74448
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