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Crystal structure of catalytic domain of human carbonic anhydrase isozyme XII with 3-[(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
- 4KP8
- Type
- protein
- Length
- 1,041 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
- E1G, ZN
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Carbonic anhydrase 12 (EC 4.2.1.1) | protein | 261 | 16% helix, 32% strand | O43570 |
| B | Carbonic anhydrase 12 (EC 4.2.1.1) | protein | 259 | 16% helix, 32% strand | O43570 |
| D | Carbonic anhydrase 12 (EC 4.2.1.1) | protein | 260 | 17% helix, 32% strand | O43570 |
Ligands and binding sites
- E1G · 3-[(pyrimidin-2-ylsulfanyl)acetyl]benzenesulfonamide · ligand · 3 copies · chains A, B, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, D
- DMS · Dimethyl sulfoxide · additive · chains A
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.78 | 0.80 | 116 | empty |
| 2 | 328 | 0.77 | 0.88 | 46 | empty |
| 3 | 480 | 0.77 | 0.85 | 66 | empty |
| 4 | 333 | 0.74 | 0.86 | 55 | empty |
| 5 | 231 | 0.58 | 0.79 | 27 | E1G, PEG |
Interfaces
5 interfaces between chains.
- A–B · 1268 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1242 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 420 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 85 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 74 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4KP8 · 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 4KP8 · PDBe 4KP8 · UniProt O43570
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