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The crystal structure of an isochorismatase-like hydrolase from alkaliphilus metalliredigens to 2.3A
Analyse The crystal structure of an isochorismatase-like hydrolase from alkaliphilus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HB7
- Type
- protein
- Length
- 1,449 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isochorismatase hydrolase
- UniProt
- A6TWT6
- Ligands
- NA, NH4
- Pockets
- 19 · best druggability 0.87
Structure
x-ray diffraction · 8 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isochorismatase hydrolase | protein | 188 | 35% helix, 23% strand | A6TWT6 |
| C | Isochorismatase hydrolase | protein | 178 | 33% helix, 24% strand | A6TWT6 |
| B | Isochorismatase hydrolase | protein | 179 | 35% helix, 24% strand | A6TWT6 |
| D | Isochorismatase hydrolase | protein | 179 | 35% helix, 24% strand | A6TWT6 |
| E | Isochorismatase hydrolase | protein | 189 | 31% helix, 23% strand | A6TWT6 |
| F | Isochorismatase hydrolase | protein | 183 | 38% helix, 23% strand | A6TWT6 |
| G | Isochorismatase hydrolase | protein | 182 | 35% helix, 24% strand | A6TWT6 |
| H | Isochorismatase hydrolase | protein | 171 | 33% helix, 25% strand | A6TWT6 |
Ligands and binding sites
- NA · Sodium ion · metal · 5 copies · chains A, C, B, D, E, F, G, H
- NH4 · Ammonium ion · ion · 6 copies · chains A, B, C, D, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 945 | 0.87 | 0.88 | 77 | empty |
| 2 | 991 | 0.76 | 0.78 | 92 | NH4 |
| 3 | 628 | 0.70 | 0.78 | 48 | empty |
| 4 | 413 | 0.68 | 0.80 | 51 | empty |
| 5 | 138 | 0.64 | 0.86 | 20 | empty |
Interfaces
11 interfaces between chains.
- E–F · 1211 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 889 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 853 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 836 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 673 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 3HB7 · The Crystal Structure of an Isochorismatase-like Hydrolase from Alkaliphilus… · 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 A6TWT6
- Elsewhere: RCSB PDB 3HB7 · PDBe 3HB7 · UniProt A6TWT6
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