Research workbench
Inhibition of caspase-2 by a designed ankyrin repeat protein (darpin)
Analyse Inhibition of caspase-2 by a designed ankyrin repeat protein (darpin) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P2C
- Type
- protein
- Length
- 2,464 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase-2
- EC
- 3.4.22.-
- UniProt
- P42575
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 16 distinct chains · 36% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Caspase-2 (EC 3.4.22.-) | protein | 162 | 30% helix, 21% strand | P42575 |
| B, F | Caspase-2 (EC 3.4.22.-) | protein | 96 | 28% helix, 14% strand | P42575 |
| P | Caspase-2 (EC 3.4.22.-) | protein | 158 | 46% helix, 0% strand | — |
| C | Caspase-2 (EC 3.4.22.-) | protein | 161 | 31% helix, 21% strand | P42575 |
| D | Caspase-2 (EC 3.4.22.-) | protein | 98 | 28% helix, 10% strand | P42575 |
| Q | Caspase-2 (EC 3.4.22.-) | protein | 158 | 50% helix, 0% strand | — |
| E, G | Caspase-2 (EC 3.4.22.-) | protein | 160 | 25% helix, 25% strand | P42575 |
| R | Caspase-2 (EC 3.4.22.-) | protein | 157 | 49% helix, 0% strand | — |
| H | Caspase-2 (EC 3.4.22.-) | protein | 98 | 28% helix, 17% strand | P42575 |
| S | Caspase-2 (EC 3.4.22.-) | protein | 153 | 43% helix, 0% strand | — |
| I | Caspase-2 (EC 3.4.22.-) | protein | 157 | 25% helix, 20% strand | P42575 |
| J | Caspase-2 (EC 3.4.22.-) | protein | 94 | 29% helix, 15% strand | P42575 |
| T | Caspase-2 (EC 3.4.22.-) | protein | 152 | 45% helix, 0% strand | — |
| K | Caspase-2 (EC 3.4.22.-) | protein | 158 | 25% helix, 22% strand | P42575 |
| L | Caspase-2 (EC 3.4.22.-) | protein | 92 | 29% helix, 14% strand | P42575 |
| U | Caspase-2 (EC 3.4.22.-) | protein | 154 | 48% helix, 0% strand | — |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.78 | 0.86 | 62 | empty |
| 2 | 458 | 0.77 | 0.85 | 54 | empty |
| 3 | 1003 | 0.76 | 0.79 | 90 | empty |
| 4 | 948 | 0.76 | 0.79 | 85 | empty |
| 5 | 877 | 0.75 | 0.79 | 76 | empty |
Interfaces
37 interfaces between chains.
- G–H · 2703 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 2690 Ų buried · 33 hydrogen bonds · protein-protein
- E–F · 2640 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2626 Ų buried · 30 hydrogen bonds · protein-protein
- K–L · 2572 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2P2C · Inhibition of caspase-2 by a designed ankyrin repeat protein (DARPin) · the same entry in another collection · chain G against G, 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 P42575
- Elsewhere: RCSB PDB 2P2C · PDBe 2P2C · UniProt P42575
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