MolNFT v1 · #167739 · protein
DH717.1 Fab monomer in complex with MAN9 glycan
6VTU · DH717.1 heavy chain: “DH717.1 Fab monomer in complex with MAN9 glycan”. X-ray diffraction, 1 ligand (MAN), 3 pockets (best druggability 0.58). MolNFT v1 #167739 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6VTU
- Type
- protein
- Length
- 433 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DH717.1 heavy chain; DH717.1 light chain
- UniProt
- S6B291, Q6IPQ0
- Ligands
- MAN
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | DH717.1 heavy chain | protein | 220 | 7% helix, 50% strand | S6B291 |
| L | DH717.1 light chain | protein | 213 | 6% helix, 50% strand | Q6IPQ0 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 428 | 0.58 | 0.75 | 56 | empty |
| 2 | 133 | 0.39 | 0.73 | 28 | empty |
| 3 | 77 | 0.34 | 0.75 | 17 | GOL |
Interfaces
1 interface between chains.
- H–L · 1732 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6VTU · DH717.1 Fab monomer in complex with man9 glycan · the same entry in another collection · chain H against H, 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 S6B291
- Every structure of UniProt Q6IPQ0
- Elsewhere: RCSB PDB 6VTU · PDBe 6VTU · UniProt S6B291 · UniProt Q6IPQ0
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