MolNFT v1 · #57422 · protein

The crystal structure of lina

3A76 · Gamma-hexachlorocyclohexane dehydrochlorinase: “The crystal structure of lina”. X-ray diffraction, 1 ligand (SPD), 9 pockets (best druggability 0.86). MolNFT v1 #57422 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3A76
Type: protein
Length: 452 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gamma-hexachlorocyclohexane dehydrochlorinase
EC: 4.5.1.-
UniProt: P51697
Ligands: SPD
Pockets: 9 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 33% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Gamma-hexachlorocyclohexane dehydrochlorinase (EC 4.5.1.-)	protein	147	33% helix, 50% strand	P51697
B	Gamma-hexachlorocyclohexane dehydrochlorinase (EC 4.5.1.-)	protein	153	31% helix, 50% strand	P51697
C	Gamma-hexachlorocyclohexane dehydrochlorinase (EC 4.5.1.-)	protein	152	34% helix, 49% strand	P51697

Ligands and binding sites

SPD · Spermidine · ligand · 3 copies · chains A, B, C
GOL · Glycerol · additive · 3 copies · chains A, B, C

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

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	438	0.86	0.94	39	empty
2	87	0.79	0.98	18	empty
3	128	0.71	0.90	24	GOL
4	152	0.70	0.89	27	SPD
5	159	0.67	0.86	27	SPD, GOL

Interfaces

3 interfaces between chains.

B–C · 1113 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1110 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 1023 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

3A76 · The crystal structure of LinA · the same entry in another collection · chain A against A, TM-score 1.00
P51697 · AlphaFold monomer V2.0 prediction for gamma-hexachlorocyclohexane dehydrochlorinase… · a predicted model of the same protein · chain A 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 P51697
Elsewhere: RCSB PDB 3A76 · PDBe 3A76 · UniProt P51697

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