MolNFT v1 · #171842 · protein
Crystal structure of mcl-1 in complex with a neutralizing alphabody cmpx-383B
6ZIE: “Crystal structure of mcl-1 in complex with a neutralizing alphabody cmpx-383B”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.48). MolNFT v1 #171842 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ZIE
- Type
- protein
- Length
- 273 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cmpx-383B; Induced myeloid leukemia cell differentiation protein mcl- 1
- UniProt
- Q07820
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cmpx-383B | protein | 123 | 78% helix, 0% strand | — |
| B | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 150 | 76% helix, 0% strand | Q07820 |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.48 | 0.83 | 14 | empty |
| 2 | 104 | 0.44 | 0.78 | 17 | empty |
| 3 | 68 | 0.29 | 0.73 | 14 | empty |
| 4 | 53 | 0.28 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1229 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6ZIE · Crystal structure of MCL-1 in complex with a neutralizing Alphabody CMPX-383B · 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 Q07820
- Elsewhere: RCSB PDB 6ZIE · PDBe 6ZIE · UniProt Q07820
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