MolNFT v1 · #50279 · protein
Hamster chymase 2
2RDL: “Hamster chymase 2”. X-ray diffraction, 3 ligands (MSU, SO4, 0QE), 4 pockets (best druggability 0.52). MolNFT v1 #50279 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2RDL
- Type
- protein
- Length
- 460 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chymase 2; Methoxysuccinyl-ala-ala-pro-ala-chloromethylketone inhibitor
- UniProt
- O70164
- Ligands
- MSU, SO4, 0QE
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Chymase 2 | protein | 226 | 9% helix, 39% strand | O70164 |
| I, J | Methoxysuccinyl-ala-ala-pro-ala-chloromethylketone inhibitor | protein | 4 | 0% helix, 50% strand | — |
Ligands and binding sites
- MSU · Succinic acid monomethyl ester · ligand · 2 copies · chains A, B, I, J
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- 0QE · Chloromethane · ion · 2 copies · chains A, I, B, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.52 | 0.81 | 25 | MSU |
| 2 | 186 | 0.47 | 0.75 | 30 | MSU |
| 3 | 61 | 0.42 | 0.82 | 16 | empty |
| 4 | 57 | 0.29 | 0.74 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–B · 513 Ų buried · 7 hydrogen bonds · protein-protein
- A–I · 327 Ų buried · 10 hydrogen bonds · protein-protein
- B–J · 286 Ų buried · 9 hydrogen bonds · protein-protein
- B–I · 40 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 covalent, 2 modified (disulfide, covalent ligand, nonstandard).
Compared structures
- 2RDL · Hamster Chymase 2 · 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 O70164
- Elsewhere: RCSB PDB 2RDL · PDBe 2RDL · UniProt O70164
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