MolNFT v1 · #102154 · protein
Crystal structure of the T1L reovirus attachment protein SIGMA1 in complex with junctional adhesion molecule-a
4ODB · Outer capsid protein sigma-1: “Crystal structure of the T1L reovirus attachment protein SIGMA1 in complex with junctional adhesion molecule-a”. X-ray diffraction, 10 pockets (best druggability 0.86). MolNFT v1 #102154 on GenesisL1…
- PDB
- 4ODB
- Type
- protein
- Length
- 792 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer capsid protein sigma-1; Junctional adhesion molecule a
- UniProt
- P04506, Q9Y624
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Outer capsid protein sigma-1 | protein | 162 | 5% helix, 58% strand | P04506 |
| D, E, F | Junctional adhesion molecule a | protein | 102 | 6% helix, 58% strand | Q9Y624 |
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.86 | 0.97 | 33 | empty |
| 2 | 171 | 0.61 | 0.83 | 37 | empty |
| 3 | 125 | 0.51 | 0.81 | 24 | empty |
| 4 | 147 | 0.51 | 0.80 | 22 | empty |
| 5 | 76 | 0.37 | 0.77 | 15 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1307 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1301 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1288 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 839 Ų buried · 22 hydrogen bonds · protein-protein
- B–E · 837 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4ODB · Crystal structure of the T1L reovirus attachment protein sigma1 in complex with… · the same entry in another collection · chain B against B, TM-score 1.00
- Q9Y624 · AlphaFold monomer V2.0 prediction for junctional adhesion molecule a (Q9Y624) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 P04506
- Every structure of UniProt Q9Y624
- Elsewhere: RCSB PDB 4ODB · PDBe 4ODB · UniProt P04506 · UniProt Q9Y624
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