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Crystal structure of a highly thermostable carbonic anhydrase from persephonella marina ex-H1
Analyse Crystal structure of a highly thermostable carbonic anhydrase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IM3
- Type
- protein
- Length
- 1,332 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbonic anhydrase (carbonate dehydratase)
- EC
- 4.2.1.1
- UniProt
- C0QRB5
- Ligands
- AZM, CA, ZN
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Carbonic anhydrase (carbonate dehydratase) (EC 4.2.1.1) | protein | 222 | 18% helix, 39% strand | C0QRB5 |
Ligands and binding sites
- AZM · 5-acetamido-1,3,4-thiadiazole-2-sulfonamide · ligand · 6 copies · chains A, B, C, D, E, F
- CA · Calcium ion · metal · 16 copies · chains A, F, B, E, C, D
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- PG4 · Tetraethylene glycol · additive · 2 copies · chains B, E, A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 501 | 0.74 | 0.83 | 55 | CA, PG4 |
| 2 | 233 | 0.74 | 0.89 | 28 | CA, PG4 |
| 3 | 614 | 0.73 | 0.81 | 58 | empty |
| 4 | 673 | 0.73 | 0.80 | 53 | empty |
| 5 | 50 | 0.68 | 0.97 | 15 | empty |
Interfaces
11 interfaces between chains.
- A–B · 1077 Ų buried · 20 hydrogen bonds · protein-protein
- A–F · 556 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 556 Ų buried · 16 hydrogen bonds · protein-protein
- D–F · 281 Ų buried · 7 hydrogen bonds · protein-protein
- C–F · 186 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6IM3 · Crystal structure of a highly thermostable carbonic anhydrase from Persephonella marina… · 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 C0QRB5
- Elsewhere: RCSB PDB 6IM3 · PDBe 6IM3 · UniProt C0QRB5
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