Research workbench
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
- 6IM1
- 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
- CA, ZN
- Pockets
- 17 · best druggability 0.76
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
- CA · Calcium ion · metal · 15 copies · chains A, F, B, E, D
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- PG4 · Tetraethylene glycol · additive · 4 copies · chains A, F, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 800 | 0.76 | 0.80 | 70 | empty |
| 2 | 493 | 0.75 | 0.83 | 53 | CA, PG4 |
| 3 | 530 | 0.74 | 0.82 | 56 | CA, PG4 |
| 4 | 53 | 0.72 | 0.99 | 16 | empty |
| 5 | 492 | 0.72 | 0.82 | 47 | empty |
Interfaces
11 interfaces between chains.
- A–B · 1055 Ų buried · 19 hydrogen bonds · protein-protein
- B–E · 557 Ų buried · 16 hydrogen bonds · protein-protein
- A–F · 550 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 296 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 190 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6IM1 · 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 6IM1 · PDBe 6IM1 · UniProt C0QRB5
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