MolNFT v1 · #100619 · protein

Crystal structure of dl-2-haloacid dehalogenase

4N2X: “Crystal structure of dl-2-haloacid dehalogenase”. X-ray diffraction, 16 pockets (best druggability 0.79). MolNFT v1 #100619 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4N2X
Type: protein
Length: 1,788 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dl-2-haloacid dehalogenase
EC: 3.8.1.10
UniProt: A6BM74
Pockets: 16 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 61% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, E, F, G	Dl-2-haloacid dehalogenase (EC 3.8.1.10)	protein	298	61% helix, 1% strand	A6BM74

Ligands and binding sites

GOL · Glycerol · additive · 12 copies · chains A, D, B, G, F, E

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

Pockets

16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	169	0.79	0.95	43	empty
2	188	0.79	0.94	44	empty
3	167	0.78	0.94	41	empty
4	367	0.69	0.82	49	GOL
5	445	0.66	0.79	48	GOL

Interfaces

9 interfaces between chains.

F–G · 1928 Å² buried · 28 hydrogen bonds · protein-protein
A–B · 1922 Å² buried · 27 hydrogen bonds · protein-protein
D–E · 1917 Å² buried · 28 hydrogen bonds · protein-protein
E–G · 424 Å² buried · 4 hydrogen bonds · protein-protein
B–G · 420 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

4N2X · Crystal Structure of DL-2-haloacid dehalogenase · the same entry in another collection · 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 A6BM74
Elsewhere: RCSB PDB 4N2X · PDBe 4N2X · UniProt A6BM74

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