Research workbench
Crystal structure of mcl-1 in complex with the BAXBH3 domain
Analyse Crystal structure of mcl-1 in complex with the BAXBH3 domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PK1
- Type
- protein
- Length
- 331 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Induced myeloid leukemia cell differentiation protein mcl- 1; Apoptosis regulator bax
- UniProt
- Q07820, Q07812
- Ligands
- CD
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 140 | 77% helix, 0% strand | Q07820 |
| B, D | Apoptosis regulator bax | protein | 27 | 85% helix, 0% strand | Q07812 |
| C | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 137 | 78% helix, 0% strand | Q07820 |
Ligands and binding sites
- CD · Cadmium ion · metal · 18 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 444 | 0.65 | 0.78 | 32 | CD |
| 2 | 61 | 0.30 | 0.75 | 13 | empty |
| 3 | 52 | 0.27 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 937 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 933 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 395 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3PK1 · Crystal structure of Mcl-1 in complex with the BaxBH3 domain · the same entry in another collection · chain A against A, TM-score 1.00
- Q07820 · AlphaFold monomer V2.0 prediction for induced myeloid leukemia cell differentiation… · a predicted model of the same protein · chain A against A, TM-score 0.96
- Q07812 · AlphaFold monomer V2.0 prediction for apoptosis regulator bax (Q07812) · a predicted model of the same protein · chain B against A, TM-score 0.71
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 Q07820
- Every structure of UniProt Q07812
- Elsewhere: RCSB PDB 3PK1 · PDBe 3PK1 · UniProt Q07820 · UniProt Q07812
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