Research workbench
Crystal structure of catalytic domain of human carbonic anhydrase isozyme XII with 2-chloro-4-[(pyrimidin-2-ylsulfanyl) ACETYL]BENZENESULFONAMIDE
Analyse Crystal structure of catalytic domain of human carbonic anhydrase isozyme XII… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KP5
- Type
- protein
- Length
- 1,042 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbonic anhydrase 12
- EC
- 4.2.1.1
- UniProt
- O43570
- Ligands
- E1F, ZN, SO4
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Carbonic anhydrase 12 (EC 4.2.1.1) | protein | 261 | 16% helix, 32% strand | O43570 |
| C, D | Carbonic anhydrase 12 (EC 4.2.1.1) | protein | 260 | 15% helix, 32% strand | O43570 |
Ligands and binding sites
- E1F · 2-chloro-4-[(pyrimidin-2-ylsulfanyl) acetyl]benzenesulfonamide · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains C
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.85 | 0.86 | 128 | empty |
| 2 | 789 | 0.85 | 0.87 | 93 | empty |
| 3 | 205 | 0.60 | 0.82 | 34 | EDO |
| 4 | 225 | 0.60 | 0.81 | 28 | E1F, EDO |
| 5 | 209 | 0.60 | 0.81 | 29 | E1F, EDO |
Interfaces
4 interfaces between chains.
- A–B · 1171 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1124 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 479 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 312 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4KP5 · Crystal structure of catalytic domain of human carbonic anhydrase isozyme XII with… · the same entry in another collection · chain D against D, TM-score 1.00
- O43570 · AlphaFold monomer V2.0 prediction for carbonic anhydrase 12 (O43570) · a predicted model of the same protein · 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 O43570
- Elsewhere: RCSB PDB 4KP5 · PDBe 4KP5 · UniProt O43570
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