MolNFT v1 · #137715 · protein
Mcl-1 in complex with bim-H3PC-rt
5VX2 · Induced myeloid leukemia cell differentiation protein mcl-1…: “Mcl-1 in complex with bim-H3PC-rt”. X-ray diffraction, 2 pockets (best druggability 0.61). MolNFT v1 #137715 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5VX2
- Type
- protein
- Length
- 349 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Induced myeloid leukemia cell differentiation protein mcl-1 HOMOLOG,INDUCED myeloid…
- UniProt
- P97287, Q07820, O43521
- Pockets
- 2 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 82% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Induced myeloid leukemia cell differentiation protein mcl-1 HOMOLOG,INDUCED myeloid leukemia cell differentiation protein mcl-1 chimera | protein | 151 | 79% helix, 0% strand | P97287, Q07820 |
| B | BCL-2-like protein 11 | protein | 23 | 91% helix, 0% strand | O43521 |
| C | Induced myeloid leukemia cell differentiation protein mcl-1 HOMOLOG,INDUCED myeloid leukemia cell differentiation protein mcl-1 chimera | protein | 150 | 81% helix, 0% strand | P97287, Q07820 |
| D | BCL-2-like protein 11 | protein | 25 | 92% helix, 0% strand | O43521 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.61 | 0.78 | 30 | empty |
| 2 | 52 | 0.35 | 0.79 | 15 | empty |
Interfaces
6 interfaces between chains.
- C–D · 997 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 981 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 276 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 257 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 234 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 5VX2 · Mcl-1 in complex with Bim-h3Pc-RT · the same entry in another collection · chain D against D, TM-score 1.00
- P97287 · AlphaFold monomer V2.0 prediction for induced myeloid leukemia cell differentiation… · a predicted model of the same protein · chain C against A, TM-score 0.98
- O43521 · AlphaFold monomer V2.0 prediction for BCL-2-like protein 11 (O43521) · a predicted model of the same protein · chain B against A, TM-score 0.73
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
- Every structure of UniProt Q07820
- Every structure of UniProt O43521
- Elsewhere: RCSB PDB 5VX2 · PDBe 5VX2 · UniProt P97287 · UniProt Q07820 · UniProt O43521
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