Research workbench
Crystal structure of a DM9 domain containing protein from crassostrea gigas with K43A mutation
Analyse Crystal structure of a DM9 domain containing protein from crassostrea gigas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MH3
- Type
- protein
- Length
- 1,716 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Natterin-3
- UniProt
- K1QRB6
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 62% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Natterin-3 | protein | 143 | 0% helix, 62% strand | K1QRB6 |
Ligands and binding sites
- GOL · Glycerol · additive · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.83 | 0.96 | 27 | empty |
| 2 | 222 | 0.83 | 0.96 | 27 | empty |
| 3 | 313 | 0.80 | 0.90 | 42 | empty |
| 4 | 489 | 0.76 | 0.84 | 56 | GOL |
| 5 | 1055 | 0.74 | 0.77 | 112 | GOL |
Interfaces
12 interfaces between chains.
- A–B · 1191 Ų buried · 19 hydrogen bonds · protein-protein
- G–I · 1173 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 1158 Ų buried · 19 hydrogen bonds · protein-protein
- F–J · 1157 Ų buried · 18 hydrogen bonds · protein-protein
- C–H · 420 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5MH3 · Crystal structure of a DM9 domain containing protein from Crassostrea gigas with K43A… · 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 K1QRB6
- Elsewhere: RCSB PDB 5MH3 · PDBe 5MH3 · UniProt K1QRB6
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