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Molecular structure of a thermostable and a zinc ion binding gamma- class carbonic anhydrase
Analyse Molecular structure of a thermostable and a zinc ion binding gamma- class… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IVE
- Type
- protein
- Length
- 1,003 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferripyochelin-binding protein
- UniProt
- Q5SH51
- Ligands
- ZN, PO4
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Ferripyochelin-binding protein | protein | 168 | 8% helix, 43% strand | Q5SH51 |
| B | Ferripyochelin-binding protein | protein | 165 | 8% helix, 42% strand | Q5SH51 |
| C | Ferripyochelin-binding protein | protein | 168 | 9% helix, 43% strand | Q5SH51 |
| D | Ferripyochelin-binding protein | protein | 167 | 9% helix, 43% strand | Q5SH51 |
| E | Ferripyochelin-binding protein | protein | 167 | 8% helix, 43% strand | Q5SH51 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 994 | 0.78 | 0.80 | 115 | PO4 |
| 2 | 66 | 0.70 | 0.96 | 29 | empty |
| 3 | 65 | 0.69 | 0.96 | 29 | empty |
| 4 | 258 | 0.58 | 0.78 | 37 | PO4 |
| 5 | 292 | 0.58 | 0.77 | 41 | PO4 |
Interfaces
8 interfaces between chains.
- A–C · 1279 Ų buried · 23 hydrogen bonds · protein-protein
- D–F · 1179 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1170 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1163 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1148 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6IVE · Molecular structure of a thermostable and a Zinc ion binding gamma-class carbonic… · the same entry in another collection · chain E against E, 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 Q5SH51
- Elsewhere: RCSB PDB 6IVE · PDBe 6IVE · UniProt Q5SH51
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