MolNFT v1 · #52732 · protein
Canine adenovirus type 2 fibre head in complex with car domain D1 and sialic acid
2W9L · Coxsackievirus and adenovirus receptor: “Canine adenovirus type 2 fibre head in complex with car domain D1 and sialic acid”. X-ray diffraction, 3 ligands (GL0, SIA, GAL), 20 pockets (best druggability 0.84). MolNFT v1 #52732 on…
- PDB
- 2W9L
- Type
- protein
- Length
- 3,627 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coxsackievirus and adenovirus receptor; Fibre protein
- UniProt
- P78310, Q65914
- Ligands
- GL0, SIA, GAL
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 8 distinct chains · 7% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, Z | Coxsackievirus and adenovirus receptor | protein | 117 | 5% helix, 44% strand | P78310 |
| B | Coxsackievirus and adenovirus receptor | protein | 117 | 8% helix, 44% strand | P78310 |
| C, D, E, F, H, I, L, M, N, Q, R, S | Fibre protein | protein | 182 | 8% helix, 45% strand | Q65914 |
| G, J, P, X | Coxsackievirus and adenovirus receptor | protein | 123 | 7% helix, 50% strand | P78310 |
| K | Coxsackievirus and adenovirus receptor | protein | 123 | 7% helix, 48% strand | P78310 |
| O | Coxsackievirus and adenovirus receptor | protein | 118 | 8% helix, 52% strand | P78310 |
| T, Y | Coxsackievirus and adenovirus receptor | protein | 119 | 8% helix, 49% strand | P78310 |
| V | Coxsackievirus and adenovirus receptor | protein | 121 | 7% helix, 45% strand | P78310 |
Ligands and binding sites
- GL0 · beta-D-gulopyranose · ligand · 2 copies · chains F
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 12 copies · chains C, D, E, F, H, I, L, M, N, Q, R, S
- GAL · beta-D-galactopyranose · sugar · 10 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.84 | 0.85 | 93 | empty |
| 2 | 645 | 0.83 | 0.88 | 68 | empty |
| 3 | 628 | 0.83 | 0.88 | 64 | empty |
| 4 | 673 | 0.82 | 0.87 | 64 | empty |
| 5 | 643 | 0.82 | 0.87 | 64 | empty |
Interfaces
37 interfaces between chains.
- C–I · 1197 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1190 Ų buried · 26 hydrogen bonds · protein-protein
- Q–S · 1190 Ų buried · 23 hydrogen bonds · protein-protein
- H–I · 1185 Ų buried · 22 hydrogen bonds · protein-protein
- L–N · 1181 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 2W9L · Canine adenovirus type 2 fibre head in complex with car domain D1 and sialic acid · the same entry in another collection · chain J against J, 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 P78310
- Every structure of UniProt Q65914
- Elsewhere: RCSB PDB 2W9L · PDBe 2W9L · UniProt P78310 · UniProt Q65914
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