MolNFT v1 · #173176 · protein
Rhinovirus A2 2A protease in complex with ZVAM.FMK
7ARA: “Rhinovirus A2 2A protease in complex with ZVAM.FMK”. X-ray diffraction, 3 ligands (S7N, S7Q, ZN), 2 pockets (best druggability 0.57). MolNFT v1 #173176 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7ARA
- Type
- protein
- Length
- 278 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2A protease
- EC
- 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- P04936
- Ligands
- S7N, S7Q, ZN
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2A protease (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 139 | 5% helix, 50% strand | P04936 |
Ligands and binding sites
- S7N · (phenylmethyl) ~{N}-[(2~{R})-3-methyl-1-[[(2~{S})-1-[[(3~{S})-1-methylsulfanyl-4-oxidanylidene-pentan-3-yl]amino]-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-butan-2-yl]carbamate · ligand · chains A
- S7Q · (phenylmethyl) ~{N}-[(2~{S})-3-methyl-1-[[(2~{R})-1-[[(3~{R})-1-methylsulfanyl-4-oxidanylidene-pentan-3-yl]amino]-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-butan-2-yl]carbamate · ligand · chains B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 249 | 0.57 | 0.78 | 35 | S7N |
| 2 | 128 | 0.41 | 0.75 | 23 | S7Q |
Interfaces
1 interface between chains.
- A–B · 763 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7ARA · Rhinovirus A2 2A protease in complex with zVAM.fmk · 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 P04936
- Elsewhere: RCSB PDB 7ARA · PDBe 7ARA · UniProt P04936
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