Research workbench
Crystal structure of amidohydrolase EAJ56179
Analyse Crystal structure of amidohydrolase EAJ56179 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MKV
- Type
- protein
- Length
- 3,305 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative amidohydrolase
- Ligands
- ZN, SO4, CO3
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative amidohydrolase | protein | 414 | 32% helix, 22% strand | — |
| B, C, D, E, F, G, H | Putative amidohydrolase | protein | 413 | 33% helix, 24% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 13 copies · chains A, B, C, D, E, G, H
- CO3 · Carbonate ion · ion · 2 copies · chains F, G
- GOL · Glycerol · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 943 | 0.83 | 0.85 | 106 | ZN, SO4, GOL |
| 2 | 1026 | 0.83 | 0.84 | 116 | SO4, CO3 |
| 3 | 1004 | 0.83 | 0.84 | 118 | ZN, CO3, SO4 |
| 4 | 1133 | 0.83 | 0.84 | 136 | ZN, SO4, GOL |
| 5 | 90 | 0.76 | 0.98 | 24 | empty |
Interfaces
16 interfaces between chains.
- C–F · 921 Ų buried · 10 hydrogen bonds · protein-protein
- F–G · 915 Ų buried · 14 hydrogen bonds · protein-protein
- A–G · 915 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 915 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 907 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified, 4 disulfide (carboxylation, disulfide).
Compared structures
- 3MKV · Crystal structure of amidohydrolase eaj56179 · 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
- Elsewhere: RCSB PDB 3MKV · PDBe 3MKV
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