Research workbench
The structure of mbp-MCL1 bound to ligand 5 at 1.9A
Analyse The structure of mbp-MCL1 bound to ligand 5 at 1.9A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WMW
- Type
- protein
- Length
- 514 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mbp-MCL1 chimera protein
- UniProt
- P0AEX9, Q07820
- Ligands
- 3R6, GLC, MG
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mbp-MCL1 chimera protein | protein | 514 | 56% helix, 14% strand | P0AEX9, Q07820 |
Ligands and binding sites
- 3R6 · 2-hydroxy-5-(methylsulfanyl)benzoic acid · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
- MG · Magnesium ion · metal · chains A
- FMT · Formic acid · additive · 7 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.71 | 0.86 | 29 | GLC, FMT |
| 2 | 481 | 0.65 | 0.78 | 52 | empty |
| 3 | 64 | 0.47 | 0.84 | 13 | empty |
| 4 | 101 | 0.38 | 0.74 | 12 | 3R6 |
| 5 | 60 | 0.33 | 0.76 | 16 | empty |
Compared structures
- 4WMW · The structure of MBP-MCL1 bound to ligand 5 at 1.9A · 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 4WMW · PDBe 4WMW · UniProt P0AEX9 · UniProt Q07820
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