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The X-ray crystallographic structure of beta carbonic anhydrase from the C3 dicot pisum sativum
Analyse The X-ray crystallographic structure of beta carbonic anhydrase from the C3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EKJ
- Type
- protein
- Length
- 1,708 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-carbonic anhydrase
- EC
- 4.2.1.1
- UniProt
- P17067
- Ligands
- ZN, CU, CL, AZI
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 7 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-carbonic anhydrase (EC 4.2.1.1) | protein | 210 | 48% helix, 16% strand | P17067 |
| B | Beta-carbonic anhydrase (EC 4.2.1.1) | protein | 213 | 48% helix, 20% strand | P17067 |
| C | Beta-carbonic anhydrase (EC 4.2.1.1) | protein | 217 | 46% helix, 19% strand | P17067 |
| D, H | Beta-carbonic anhydrase (EC 4.2.1.1) | protein | 211 | 47% helix, 16% strand | P17067 |
| E | Beta-carbonic anhydrase (EC 4.2.1.1) | protein | 212 | 48% helix, 16% strand | P17067 |
| F | Beta-carbonic anhydrase (EC 4.2.1.1) | protein | 214 | 47% helix, 19% strand | P17067 |
| G | Beta-carbonic anhydrase (EC 4.2.1.1) | protein | 220 | 45% helix, 20% strand | P17067 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
- AZI · Azide ion · ion · 4 copies · chains A, D, E, H
- ACT · Acetate ion · additive · 9 copies · chains A, B, C, D, E, F, G, H
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, D, E, H
- CIT · Citric acid · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.77 | 0.99 | 24 | CL |
| 2 | 93 | 0.76 | 0.97 | 25 | CL |
| 3 | 83 | 0.75 | 0.98 | 24 | CL |
| 4 | 82 | 0.75 | 0.98 | 21 | CL |
| 5 | 420 | 0.62 | 0.77 | 43 | empty |
Interfaces
12 interfaces between chains.
- E–F · 3495 Ų buried · 54 hydrogen bonds · protein-protein
- C–D · 3443 Ų buried · 58 hydrogen bonds · protein-protein
- G–H · 3417 Ų buried · 56 hydrogen bonds · protein-protein
- A–B · 3398 Ų buried · 53 hydrogen bonds · protein-protein
- B–C · 1118 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 1EKJ · The X-ray crystallographic structure of beta carbonic anhydrase from the C3 dicot pisum… · the same entry in another collection · chain H against H, TM-score 1.00
- P17067 · AlphaFold monomer V2.0 prediction for carbonic anhydrase, chloroplastic (P17067) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 P17067
- Elsewhere: RCSB PDB 1EKJ · PDBe 1EKJ · UniProt P17067
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