Research workbench
Oxidized, active structure of the beta-carboxysomal gamma-carbonic anhydrase, ccmm
Analyse Oxidized, active structure of the beta-carboxysomal gamma-carbonic anhydrase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KWC
- Type
- protein
- Length
- 1,228 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbon dioxide concentrating mechanism protein
- EC
- 4.2.1.1
- UniProt
- Q8DKB5
- Ligands
- ZN, CL
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E | Carbon dioxide concentrating mechanism protein (EC 4.2.1.1) | protein | 205 | 19% helix, 34% strand | Q8DKB5 |
| B, F | Carbon dioxide concentrating mechanism protein (EC 4.2.1.1) | protein | 204 | 18% helix, 34% strand | Q8DKB5 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, C, B, D, F, E
- CL · Chloride ion · ion · 2 copies · chains A, B, C, D, E, F
- IPA · Isopropyl alcohol · additive · 7 copies · chains A, B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.78 | 0.98 | 33 | CL |
| 2 | 100 | 0.78 | 0.98 | 33 | CL |
| 3 | 372 | 0.66 | 0.80 | 38 | empty |
| 4 | 331 | 0.65 | 0.80 | 39 | empty |
| 5 | 102 | 0.61 | 0.87 | 17 | empty |
Interfaces
12 interfaces between chains.
- A–B · 1351 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1335 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1316 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1304 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 1274 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3KWC · Oxidized, active structure of the beta-carboxysomal gamma-Carbonic Anhydrase, CcmM · the same entry in another collection · chain F against F, TM-score 1.00
- Q8DKB5 · AlphaFold monomer V2.0 prediction for carboxysome assembly protein ccmm (Q8DKB5) · a predicted model of the same protein · chain E 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 Q8DKB5
- Elsewhere: RCSB PDB 3KWC · PDBe 3KWC · UniProt Q8DKB5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.