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Crystal structure of human carbonic anhydrase isozyme XII with 4-(1H- benzimidazol-1-YLACETYL)BENZENESULFONAMIDE

Analyse Crystal structure of human carbonic anhydrase isozyme XII with 4-(1H… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5LL5
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: 6YH, ZN
Pockets: 9 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 16% 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	16% helix, 32% strand	O43570

Ligands and binding sites

6YH · 4-[2-(benzimidazol-1-yl)ethanoyl]benzenesulfonamide · ligand · 4 copies · chains A, B, C, D
ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, C, 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, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1006	0.84	0.85	134	empty
2	1104	0.82	0.83	121	EDO
3	76	0.70	0.96	25	empty
4	213	0.59	0.80	29	6YH, EDO
5	194	0.59	0.81	28	6YH, EDO

Interfaces

5 interfaces between chains.

A–B · 1155 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 1138 Å² buried · 24 hydrogen bonds · protein-protein
B–D · 486 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 282 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 15 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5LL5 · 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 5LL5 · PDBe 5LL5 · UniProt O43570

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