Research workbench
Structure of mbp-MCL1 bound to ligand 2 at 1.55A
Analyse Structure of mbp-MCL1 bound to ligand 2 at 1.55A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WMU
- Type
- protein
- Length
- 516 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mbp-MCL1 chimera PROTEIN,INDUCED myeloid leukemia cell differentiation protein mcl-1
- UniProt
- P0AEX9, Q07820
- Ligands
- 19H, GLC, MG, NA
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mbp-MCL1 chimera PROTEIN,INDUCED myeloid leukemia cell differentiation protein mcl-1 | protein | 516 | 55% helix, 14% strand | P0AEX9, Q07820 |
Ligands and binding sites
- 19H · 6-chloro-3-[3-(4-chloro-3,5-dimethylphenoxy)propyl]-1H-indole-2-carboxylic acid · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains A
- FMT · Formic acid · additive · 13 copies · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.71 | 0.86 | 29 | GLC, FMT |
| 2 | 442 | 0.66 | 0.79 | 48 | EDO |
| 3 | 133 | 0.60 | 0.84 | 18 | 19H |
| 4 | 56 | 0.40 | 0.81 | 14 | empty |
Compared structures
- 4WMU · STRUCTURE OF MBP-MCL1 BOUND TO ligand 2 AT 1.55A · 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 P0AEX9
- Every structure of UniProt Q07820
- Elsewhere: RCSB PDB 4WMU · PDBe 4WMU · UniProt P0AEX9 · UniProt Q07820
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