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Crystal structure of human carbonic anhydrase isozyme XII with 4- chloro-2-(cyclohexylamino)-N-(2-hydroxyethyl)-5-sulfamoyl-benzamide

Analyse Crystal structure of human carbonic anhydrase isozyme XII with 4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6G5L
Type: protein
Length: 1,044 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: EM5, ZN
Pockets: 9 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 17% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Carbonic anhydrase 12 (EC 4.2.1.1)	protein	261	17% helix, 32% strand	O43570

Ligands and binding sites

EM5 · 4-chloranyl-2-(cyclohexylamino)-~{N}-(2-hydroxyethyl)-5-sulfamoyl-benzamide · ligand · 4 copies · chains A, B, C, D
ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · 12 copies · chains A, B, C, D
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1053	0.85	0.86	127	EDO
2	603	0.78	0.84	70	EDO
3	225	0.74	0.89	38	empty
4	603	0.65	0.75	48	EDO
5	199	0.59	0.81	25	EM5, EDO

Interfaces

5 interfaces between chains.

C–D · 1175 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1106 Å² buried · 25 hydrogen bonds · protein-protein
B–D · 470 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 301 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 27 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6G5L · Crystal structure 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 6G5L · PDBe 6G5L · UniProt O43570

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