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The crystal structure of D-2-halacid dehalogenase mutant

Analyse The crystal structure of D-2-halacid dehalogenase mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5H01
Type: protein
Length: 1,168 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: (R)-2-haloacid dehalogenase
EC: 3.8.1.9
UniProt: Q52086
Pockets: 11 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 65% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	(R)-2-haloacid dehalogenase (EC 3.8.1.9)	protein	292	65% helix, 1% strand	Q52086

Pockets

11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	803	0.74	0.79	79	empty
2	57	0.72	0.99	18	empty
3	539	0.68	0.78	55	empty
4	64	0.67	0.94	25	empty
5	466	0.67	0.79	51	empty

Interfaces

6 interfaces between chains.

A–D · 1163 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 1149 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1044 Å² buried · 31 hydrogen bonds · protein-protein
C–D · 1037 Å² buried · 29 hydrogen bonds · protein-protein
B–D · 101 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5H01 · The crystal structure of D-2-halacid dehalogenase mutant · the same entry in another collection · chain A against A, TM-score 1.00
Q52086 · AlphaFold monomer V2.0 prediction for (R)-2-haloacid dehalogenase (Q52086) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q52086
Elsewhere: RCSB PDB 5H01 · PDBe 5H01 · UniProt Q52086

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