MolNFT v1 · #156661 · protein
Human mcl-1 in complex with the designed peptide DM1
6MBD · Induced myeloid leukemia cell differentiation protein mcl- 1: “Human mcl-1 in complex with the designed peptide DM1”. X-ray diffraction, 1 ligand (ZN), 1 pocket (best druggability 0.53). MolNFT v1 #156661 on GenesisL1: 3D structure…
- PDB
- 6MBD
- Type
- protein
- Length
- 355 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Induced myeloid leukemia cell differentiation protein mcl- 1; DM1
- UniProt
- Q07820
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 155 | 74% helix, 0% strand | Q07820 |
| B | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 154 | 74% helix, 0% strand | Q07820 |
| C, D | DM1 | protein | 23 | 91% helix, 0% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.53 | 0.75 | 35 | empty |
Interfaces
5 interfaces between chains.
- A–C · 982 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 971 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 515 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 72 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 67 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6MBD · Human Mcl-1 in complex with the designed peptide dM1 · the same entry in another collection · chain D against D, 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 6MBD · PDBe 6MBD · UniProt Q07820
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