Research workbench
Crystal structure of mixbm
Analyse Crystal structure of mixbm in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EHG
- Type
- protein
- Length
- 1,072 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mixbm
- UniProt
- A0A0U4F749
- Ligands
- CA, SO4
- Pockets
- 7 · best druggability 0.47
Structure
x-ray diffraction · 6 distinct chains · 3% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mixbm | protein | 134 | 2% helix, 59% strand | A0A0U4F749 |
| B | Mixbm | protein | 133 | 2% helix, 60% strand | A0A0U4F749 |
| C, D | Mixbm | protein | 134 | 4% helix, 60% strand | A0A0U4F749 |
| E | Mixbm | protein | 136 | 4% helix, 59% strand | A0A0U4F749 |
| F | Mixbm | protein | 135 | 4% helix, 59% strand | A0A0U4F749 |
| G, H | Mixbm | protein | 133 | 2% helix, 60% strand | A0A0U4F749 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 9 copies · chains A, B, C, D, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.47 | 0.75 | 28 | empty |
| 2 | 110 | 0.40 | 0.76 | 28 | empty |
| 3 | 107 | 0.39 | 0.75 | 26 | empty |
| 4 | 105 | 0.35 | 0.73 | 20 | empty |
| 5 | 64 | 0.31 | 0.75 | 18 | empty |
Interfaces
8 interfaces between chains.
- F–G · 540 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 395 Ų buried · 15 hydrogen bonds · protein-protein
- E–G · 393 Ų buried · 14 hydrogen bonds · protein-protein
- F–H · 370 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 356 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7EHG · Crystal Structure of MiXBM · 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 A0A0U4F749
- Elsewhere: RCSB PDB 7EHG · PDBe 7EHG · UniProt A0A0U4F749
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