Research workbench
Crystal structure of amidohydrolase SARO_0799 (target efi-505250) from novosphingobium aromaticivorans dsm 12444 with bound calcium
Analyse Crystal structure of amidohydrolase SARO_0799 (target efi-505250) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4INF
- Type
- protein
- Length
- 1,396 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metal-dependent hydrolase
- UniProt
- Q2GA79
- Ligands
- OXD, CA, CL
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metal-dependent hydrolase | protein | 351 | 51% helix, 10% strand | Q2GA79 |
| B | Metal-dependent hydrolase | protein | 349 | 51% helix, 10% strand | Q2GA79 |
| C, D | Metal-dependent hydrolase | protein | 348 | 52% helix, 10% strand | Q2GA79 |
Ligands and binding sites
- OXD · Oxalic acid · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 16 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.78 | 0.98 | 32 | CL, OXD |
| 2 | 91 | 0.76 | 0.98 | 27 | CL, OXD |
| 3 | 90 | 0.74 | 0.96 | 26 | CL, OXD |
| 4 | 54 | 0.69 | 0.97 | 19 | CL, OXD |
| 5 | 50 | 0.50 | 0.87 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–B · 3030 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 3018 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4INF · Crystal structure of amidohydrolase saro_0799 (target efi-505250) from novosphingobium… · 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 Q2GA79
- Elsewhere: RCSB PDB 4INF · PDBe 4INF · UniProt Q2GA79
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