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Crystal structure of human carbonic anhydrase isozyme xiii with 2- chloro-4-[(pyrimidin-2-YLSULFANYL)ACETYL]BENZENESULFONAMIDE

Analyse Crystal structure of human carbonic anhydrase isozyme xiii with 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4KNN
Type: protein
Length: 516 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: E1F, ZN
Pockets: 5 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 16% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A	Carbonic anhydrase 13 (EC 4.2.1.1)	protein	258	16% helix, 31% strand	Q8N1Q1

Ligands and binding sites

E1F · 2-chloro-4-[(pyrimidin-2-ylsulfanyl) acetyl]benzenesulfonamide · ligand · 2 copies · chains B, A
ZN · Zinc ion · metal · 2 copies · chains B, A
EDO · 1,2-ethanediol · additive · 3 copies · chains B, A
ACY · Acetic acid · additive · 3 copies · chains B
CIT · Citric acid · additive · 2 copies · chains B, A
PEG · Di(hydroxyethyl)ether · additive · chains A

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	200	0.70	0.87	33	EDO
2	209	0.60	0.81	30	E1F
3	207	0.57	0.79	29	E1F
4	98	0.41	0.77	20	empty
5	93	0.35	0.74	20	empty

Interfaces

1 interface between chains.

B–A · 724 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

4KNN · Crystal structure of human carbonic anhydrase isozyme XIII with… · the same entry in another collection · chain A against A, TM-score 1.00
Q8N1Q1 · AlphaFold monomer V2.0 prediction for carbonic anhydrase 13 (Q8N1Q1) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 4KNN · PDBe 4KNN · UniProt Q8N1Q1

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