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Crystal structure of putative amidohydrolase-2 (efi-target 500288)FROM polaromonas sp. JS666
Analyse Crystal structure of putative amidohydrolase-2 (efi-target 500288)FROM… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S4T
- Type
- protein
- Length
- 2,606 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amidohydrolase 2
- UniProt
- Q12BV1
- Ligands
- SO4, CL
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amidohydrolase 2 | protein | 332 | 52% helix, 12% strand | Q12BV1 |
| B, D, F, H | Amidohydrolase 2 | protein | 324 | 52% helix, 12% strand | Q12BV1 |
| C | Amidohydrolase 2 | protein | 326 | 52% helix, 12% strand | Q12BV1 |
| E | Amidohydrolase 2 | protein | 325 | 52% helix, 12% strand | Q12BV1 |
| G | Amidohydrolase 2 | protein | 327 | 52% helix, 12% strand | Q12BV1 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 30 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · chains B
- ACT · Acetate ion · additive · 16 copies · chains A, B, C, D, E, F, G, H
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 7 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 3 copies · chains C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.76 | 0.98 | 25 | empty |
| 2 | 90 | 0.76 | 0.98 | 27 | empty |
| 3 | 87 | 0.76 | 0.98 | 27 | empty |
| 4 | 85 | 0.75 | 0.98 | 29 | empty |
| 5 | 72 | 0.73 | 0.97 | 24 | empty |
Interfaces
13 interfaces between chains.
- G–H · 3301 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 3297 Ų buried · 45 hydrogen bonds · protein-protein
- E–F · 3290 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 3288 Ų buried · 46 hydrogen bonds · protein-protein
- B–D · 556 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 72 modified (engineered).
Compared structures
- 3S4T · Crystal structure of putative amidohydrolase-2 (EFI-target 500288)from Polaromonas sp.… · 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 Q12BV1
- Elsewhere: RCSB PDB 3S4T · PDBe 3S4T · UniProt Q12BV1
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