Research workbench
MBP-Mcl1 in complex with ligand 12
Analyse MBP-Mcl1 in complex with ligand 12 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8G3T
- Type
- protein
- Length
- 518 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.83
- Source
- Homo sapiens; Serratia sp. FS14
- Molecule
- Maltodextrin-binding protein, Induced myeloid leukemia cell differentiation protein Mcl-1…
- UniProt
- A0A4P1LXE0, Q07820
- Ligands
- YLK, GLC
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · resolution 1.83 · 1 distinct chain · 55% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltodextrin-binding protein, Induced myeloid leukemia cell differentiation protein Mcl-1 chimera | protein | 518 | 55% helix, 15% strand | A0A4P1LXE0, Q07820 |
Ligands and binding sites
- YLK · (1'S,3aS,5R,16R,17S,19Z,21R,21aR)-6'-chloro-20-fluoro-21-methoxy-16,17-dimethyl-2,3,3',3a,4',16,17,18,21,21a-decahydro-2'H,6H,8H-15lambda~6~-spiro[10,12-etheno-15lambda~6~-furo[3,2-i][1,4]oxazepino[3,4-f][1,2,7]thiadiazacyclohexadecine-7,1'-naphthalene]-13,15,15(4H,14H)-trione · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
- FMT · Formic acid · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 279 | 0.70 | 0.84 | 29 | GLC |
| 2 | 493 | 0.64 | 0.77 | 38 | empty |
| 3 | 183 | 0.64 | 0.83 | 18 | YLK |
| 4 | 74 | 0.50 | 0.84 | 17 | empty |
| 5 | 58 | 0.42 | 0.82 | 14 | empty |
Compared structures
- Q07820 · AlphaFold monomer V2.0 prediction for induced myeloid leukemia cell differentiation… · a predicted model of the same protein · chain A against A, TM-score 0.30
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 A0A4P1LXE0
- Every structure of UniProt Q07820
- Elsewhere: RCSB PDB 8G3T · PDBe 8G3T · UniProt A0A4P1LXE0 · UniProt Q07820
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