Research workbench
Structure of MBP-Mcl-1 in complex with compound 8a
Analyse Structure of MBP-Mcl-1 in complex with compound 8a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QYL
- Type
- protein
- Length
- 513 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Escherichia coli; Homo sapiens
- Molecule
- Maltose/maltodextrin-binding periplasmic protein,Induced myeloid leukemia cell…
- UniProt
- P0AEY0, Q07820
- Ligands
- JLE, GLC, NA
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · resolution 2.2 · 1 distinct chain · 55% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltose/maltodextrin-binding periplasmic protein,Induced myeloid leukemia cell differentiation protein Mcl-1 | protein | 513 | 55% helix, 14% strand | P0AEY0, Q07820 |
Ligands and binding sites
- JLE · (2~{R})-2-[[6-ethyl-5-(1~{H}-indol-4-yl)thieno[2,3-d]pyrimidin-4-yl]amino]-3-phenyl-propanoic acid · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.71 | 0.84 | 30 | GLC, NA |
| 2 | 393 | 0.60 | 0.76 | 29 | empty |
| 3 | 101 | 0.44 | 0.78 | 13 | JLE |
| 4 | 62 | 0.40 | 0.80 | 15 | empty |
| 5 | 51 | 0.37 | 0.81 | 15 | empty |
Compared structures
- 6QYL · Structure of mbp-mcl-1 in complex with compound 8A · the same entry in another collection · chain A against A, TM-score 1.00
- P0AEY0 · AlphaFold monomer V2.0 prediction for MALTOSE/MALTODEXTRIN-binding periplasmic protein… · a predicted model of the same protein · chain A against A, TM-score 0.71
- 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 0.31
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 P0AEY0
- Every structure of UniProt Q07820
- Elsewhere: RCSB PDB 6QYL · PDBe 6QYL · UniProt P0AEY0 · UniProt Q07820
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