Research workbench
Caspase-3 in complex with an inhibitory darpin-3.4
Analyse Caspase-3 in complex with an inhibitory darpin-3.4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XZD
- Type
- protein
- Length
- 709 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase-3; Darpin-3.4
- EC
- 3.4.22.56
- UniProt
- P42574
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 6 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Caspase-3 (EC 3.4.22.56) | protein | 141 | 27% helix, 32% strand | P42574 |
| B | Caspase-3 (EC 3.4.22.56) | protein | 94 | 33% helix, 19% strand | P42574 |
| C | Caspase-3 (EC 3.4.22.56) | protein | 142 | 27% helix, 32% strand | P42574 |
| D | Caspase-3 (EC 3.4.22.56) | protein | 93 | 33% helix, 19% strand | P42574 |
| G | Darpin-3.4 | protein | 119 | 53% helix, 0% strand | — |
| H | Darpin-3.4 | protein | 120 | 50% helix, 0% strand | — |
Ligands and binding sites
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 3 copies · chains A, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A, B, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 329 | 0.66 | 0.80 | 37 | empty |
| 2 | 442 | 0.65 | 0.78 | 51 | MPD |
| 3 | 291 | 0.61 | 0.79 | 42 | empty |
| 4 | 82 | 0.39 | 0.77 | 20 | empty |
| 5 | 63 | 0.29 | 0.74 | 17 | empty |
Interfaces
10 interfaces between chains.
- C–D · 2204 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 2185 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 1430 Ų buried · 23 hydrogen bonds · protein-protein
- D–H · 664 Ų buried · 6 hydrogen bonds · protein-protein
- B–G · 639 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
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 P42574
- Elsewhere: RCSB PDB 2XZD · PDBe 2XZD · UniProt P42574
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