MolNFT v1 · #156074 · protein
Complex structure of bovine herpesvirus 1 glycoprotein D and bovine nectin-1 igv
6LSA · Nectin cell adhesion molecule 1: “Complex structure of bovine herpesvirus 1 glycoprotein D and bovine nectin-1 igv”. X-ray diffraction, 1 ligand (NAG), 11 pockets (best druggability 0.65). MolNFT v1 #156074 on GenesisL1: 3D…
- PDB
- 6LSA
- Type
- protein
- Length
- 706 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nectin cell adhesion molecule 1; Envelope glycoprotein D
- UniProt
- F1MQJ3, Q76PF1
- Ligands
- NAG
- Pockets
- 11 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nectin cell adhesion molecule 1 | protein | 109 | 3% helix, 53% strand | F1MQJ3 |
| F, C | Envelope glycoprotein D | protein | 244 | 16% helix, 32% strand | Q76PF1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.65 | 0.82 | 43 | empty |
| 2 | 309 | 0.65 | 0.81 | 44 | empty |
| 3 | 124 | 0.58 | 0.84 | 20 | empty |
| 4 | 153 | 0.50 | 0.78 | 23 | empty |
| 5 | 139 | 0.48 | 0.78 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–F · 1012 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 993 Ų buried · 9 hydrogen bonds · protein-protein
- F–B · 306 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 299 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 207 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6LSA · Complex structure of bovine herpesvirus 1 glycoprotein D and bovine nectin-1 IgV · the same entry in another collection · chain A against A, 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 F1MQJ3
- Every structure of UniProt Q76PF1
- Elsewhere: RCSB PDB 6LSA · PDBe 6LSA · UniProt F1MQJ3 · UniProt Q76PF1
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