MolNFT v1 · #105029 · protein
Crystal structure of human carbonic anhydrase isozyme xiii with 2- chloro-4-{[(4-methyl-6-oxo-1,6-dihydropyrimidin-2-yl) THIO]ACETYL}BENZENESULFONAMIDE
4QSJ · Carbonic anhydrase 13: “Crystal structure of human carbonic anhydrase isozyme xiii with 2…”. X-ray diffraction, 3 ligands (EWW, ZN, NI), 5 pockets (best druggability 0.67). MolNFT v1 #105029 on GenesisL1: 3D structure, binding sites…
- PDB
- 4QSJ
- Type
- protein
- Length
- 518 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbonic anhydrase 13
- EC
- 4.2.1.1
- UniProt
- Q8N1Q1
- Ligands
- EWW, ZN, NI
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Carbonic anhydrase 13 (EC 4.2.1.1) | protein | 258 | 17% helix, 31% strand | Q8N1Q1 |
| A | Carbonic anhydrase 13 (EC 4.2.1.1) | protein | 260 | 15% helix, 32% strand | Q8N1Q1 |
Ligands and binding sites
- EWW · 2-chloro-4-{[(4-methyl-6-oxo-1,6-dihydropyrimidin-2-yl)sulfanyl]acetyl}benzenesulfonamide · ligand · 2 copies · chains B, A
- ZN · Zinc ion · metal · 2 copies · chains B, A
- NI · Nickel (II) ion · metal · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B
- CIT · Citric acid · additive · 2 copies · chains B
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, A
- DMS · Dimethyl sulfoxide · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.67 | 0.84 | 37 | EDO |
| 2 | 235 | 0.60 | 0.80 | 30 | ZN, EWW |
| 3 | 192 | 0.56 | 0.79 | 26 | EWW |
| 4 | 114 | 0.43 | 0.77 | 24 | empty |
| 5 | 52 | 0.33 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- B–A · 700 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
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 Q8N1Q1
- Elsewhere: RCSB PDB 4QSJ · PDBe 4QSJ · UniProt Q8N1Q1
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