Research workbench
Mcl-1 in complex with a biphenyl cross-linked noxa peptide.
Analyse Mcl-1 in complex with a biphenyl cross-linked noxa peptide. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4G35
- Type
- protein
- Length
- 148 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Induced myeloid leukemia cell differentiation protein mcl-1 homolog; Noxa BH3 peptide…
- UniProt
- P97287
- Ligands
- ACE, 4BP, NH2
- Pockets
- 2 · best druggability 0.39
Structure
x-ray diffraction · 2 distinct chains · 82% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Induced myeloid leukemia cell differentiation protein mcl-1 homolog | protein | 129 | 81% helix, 0% strand | P97287 |
| B | Noxa BH3 peptide (cysteine-mediated cross-linked) | protein | 19 | 89% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A, B
- 4BP · 4,4'-bis(bromomethyl)biphenyl · ligand · chains A, B
- NH2 · Amino group · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.39 | 0.74 | 19 | empty |
| 2 | 81 | 0.37 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 776 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 1 d-amino (covalent ligand, D-amino acid).
Compared structures
- 4G35 · Mcl-1 in complex with a biphenyl cross-linked Noxa peptide. · the same entry in another collection · chain A against A, TM-score 1.00
- P97287 · AlphaFold monomer V2.0 prediction for induced myeloid leukemia cell differentiation… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P97287
- Elsewhere: RCSB PDB 4G35 · PDBe 4G35 · UniProt P97287
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