MolNFT v1 · #138821 · protein
Apaf-1-caspase-9 holoenzyme
5WVE · Apoptotic protease-activating factor 1: “Apaf-1-caspase-9 holoenzyme”. Electron microscopy, 3 ligands (DTP, HEM, MG), 20 pockets (best druggability 0.86). MolNFT v1 #138821 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5WVE
- Type
- protein
- Length
- 9,766 residues
- Chains
- 25
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apoptotic protease-activating factor 1; Cytochrome C; Caspase
- UniProt
- O14727, P00004, A8K7U6
- Ligands
- DTP, HEM, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 7 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M | Apoptotic protease-activating factor 1 | protein | 1144 | 25% helix, 24% strand | O14727 |
| B, D, F, H, J, L, N | Cytochrome C | protein | 104 | 41% helix, 2% strand | P00004 |
| O, P, Q, R | Apoptotic protease-activating factor 1 | protein | 91 | 76% helix, 0% strand | O14727 |
| S, T, U, V | Caspase | protein | 96 | 67% helix, 0% strand | A8K7U6 |
| W | Apoptotic protease-activating factor 1 | protein | 95 | 69% helix, 0% strand | O14727 |
| X | Apoptotic protease-activating factor 1 | protein | 92 | 77% helix, 0% strand | O14727 |
| Y | Caspase | protein | 95 | 67% helix, 0% strand | A8K7U6 |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 7 copies · chains A, C, E, G, I, K, M
- HEM · Protoporphyrin IX containing Fe · ligand · 7 copies · chains B, D, F, H, J, L, N
- MG · Magnesium ion · metal · 7 copies · chains A, C, E, G, I, K, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 816 | 0.86 | 0.88 | 114 | empty |
| 2 | 813 | 0.85 | 0.88 | 115 | empty |
| 3 | 1079 | 0.85 | 0.86 | 99 | HEM |
| 4 | 1083 | 0.85 | 0.86 | 101 | HEM |
| 5 | 992 | 0.85 | 0.85 | 96 | HEM |
Interfaces
41 interfaces between chains.
- A–M · 1536 Ų buried · 27 hydrogen bonds · protein-protein
- G–I · 1533 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1532 Ų buried · 27 hydrogen bonds · protein-protein
- I–K · 1531 Ų buried · 27 hydrogen bonds · protein-protein
- E–G · 1529 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 35 disulfide, 14 cofactor (disulfide, heme attachment).
Compared structures
- 5WVE · Apaf-1-Caspase-9 holoenzyme · the same entry in another collection · chain K against K, 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 O14727
- Every structure of UniProt P00004
- Every structure of UniProt A8K7U6
- Elsewhere: RCSB PDB 5WVE · PDBe 5WVE · UniProt O14727 · UniProt P00004 · UniProt A8K7U6
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