Research workbench
Structure of mbp-MCL1 bound to ligand 4 at 2.4A
Analyse Structure of mbp-MCL1 bound to ligand 4 at 2.4A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WMV
- Type
- protein
- Length
- 514 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mbl-MCL1 chimera protein
- UniProt
- P0AEX9, Q07820
- Ligands
- 3R4, GLC, MG, CL
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mbl-MCL1 chimera protein | protein | 514 | 55% helix, 15% strand | P0AEX9, Q07820 |
Ligands and binding sites
- 3R4 · 3-chloro-6-fluoro-1-benzothiophene-2-carboxylic acid · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 250 | 0.71 | 0.86 | 30 | GLC |
| 2 | 494 | 0.65 | 0.77 | 49 | empty |
| 3 | 58 | 0.41 | 0.81 | 18 | empty |
| 4 | 82 | 0.34 | 0.74 | 13 | 3R4 |
Compared structures
- 4WMV · STRUCTURE OF MBP-MCL1 BOUND TO ligand 4 AT 2.4A · 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 4WMV · PDBe 4WMV · UniProt P0AEX9 · UniProt Q07820
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