MolNFT v1 · #169487 · protein
Crystal structure analysis of mbp-SIN3
6XDJ · Maltodextrin-binding PROTEIN,TRANSCRIPTIONAL regulatory…: “Crystal structure analysis of mbp-SIN3”. X-ray diffraction, 2 ligands (GLC, BGC), 19 pockets (best druggability 0.79). MolNFT v1 #169487 on GenesisL1: 3D structure, binding…
- PDB
- 6XDJ
- Type
- protein
- Length
- 1,636 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltodextrin-binding PROTEIN,TRANSCRIPTIONAL regulatory protein SIN3
- UniProt
- A0A4P1LXE0, P22579
- Ligands
- GLC, BGC
- Pockets
- 19 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltodextrin-binding PROTEIN,TRANSCRIPTIONAL regulatory protein SIN3 | protein | 441 | 49% helix, 17% strand | A0A4P1LXE0, P22579 |
| B | Maltodextrin-binding PROTEIN,TRANSCRIPTIONAL regulatory protein SIN3 | protein | 438 | 49% helix, 17% strand | A0A4P1LXE0, P22579 |
| C | Maltodextrin-binding PROTEIN,TRANSCRIPTIONAL regulatory protein SIN3 | protein | 386 | 46% helix, 20% strand | A0A4P1LXE0, P22579 |
| D | Maltodextrin-binding PROTEIN,TRANSCRIPTIONAL regulatory protein SIN3 | protein | 371 | 45% helix, 18% strand | A0A4P1LXE0, P22579 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- BGC · beta-D-glucopyranose · sugar · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1106 | 0.79 | 0.81 | 92 | BGC, GLC |
| 2 | 372 | 0.75 | 0.85 | 32 | BGC, GLC |
| 3 | 392 | 0.72 | 0.83 | 32 | BGC, GLC |
| 4 | 411 | 0.71 | 0.82 | 39 | GLC |
| 5 | 517 | 0.69 | 0.79 | 70 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1950 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 273 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 220 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 31 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 13 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 P22579
- Elsewhere: RCSB PDB 6XDJ · PDBe 6XDJ · UniProt A0A4P1LXE0 · UniProt P22579
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