Research workbench
Isatin hydrolase a (iha) from labrenzia aggregata bound to benzyl benzoate
Analyse Isatin hydrolase a (iha) from labrenzia aggregata bound to benzyl benzoate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NNA
- Type
- protein
- Length
- 1,032 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isatin hydrolase a
- UniProt
- A0P0F0
- Ligands
- BZM, MN
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isatin hydrolase a | protein | 255 | 27% helix, 29% strand | A0P0F0 |
| B | Isatin hydrolase a | protein | 256 | 25% helix, 29% strand | A0P0F0 |
| C | Isatin hydrolase a | protein | 257 | 27% helix, 28% strand | A0P0F0 |
| D | Isatin hydrolase a | protein | 264 | 27% helix, 28% strand | A0P0F0 |
Ligands and binding sites
- BZM · Benzoic acid phenylmethylester · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
- 1PE · Pentaethylene glycol · additive · chains B
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.86 | 0.87 | 131 | BZM, MN, PEG |
| 2 | 139 | 0.71 | 0.90 | 35 | BZM |
| 3 | 137 | 0.68 | 0.89 | 32 | BZM |
| 4 | 74 | 0.33 | 0.75 | 22 | empty |
| 5 | 54 | 0.32 | 0.77 | 19 | empty |
Interfaces
5 interfaces between chains.
- C–D · 3449 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 3373 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 276 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 159 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 156 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5NNA · Isatin hydrolase A (IHA) from Labrenzia aggregata bound to benzyl benzoate · 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 A0P0F0
- Elsewhere: RCSB PDB 5NNA · PDBe 5NNA · UniProt A0P0F0
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