MolNFT v1 · #120425 · protein

The crystal structure of D-2-haloacid dehalogenase

5H00 · (R)-2-haloacid dehalogenase: “The crystal structure of D-2-haloacid dehalogenase”. X-ray diffraction, 10 pockets (best druggability 0.70). MolNFT v1 #120425 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5H00
Type: protein
Length: 1,158 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: 10 · best druggability 0.70

Structure

x-ray diffraction · 4 distinct chains · 66% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	(R)-2-haloacid dehalogenase (EC 3.8.1.9)	protein	291	65% helix, 1% strand	Q52086
B	(R)-2-haloacid dehalogenase (EC 3.8.1.9)	protein	292	65% helix, 1% strand	Q52086
C	(R)-2-haloacid dehalogenase (EC 3.8.1.9)	protein	289	66% helix, 1% strand	Q52086
D	(R)-2-haloacid dehalogenase (EC 3.8.1.9)	protein	286	67% helix, 1% strand	Q52086

Pockets

10 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	587	0.70	0.79	64	empty
2	516	0.68	0.79	59	empty
3	486	0.67	0.78	46	empty
4	429	0.65	0.78	36	empty
5	247	0.59	0.80	36	empty

Interfaces

6 interfaces between chains.

A–C · 1146 Å² buried · 18 hydrogen bonds · protein-protein
B–D · 1132 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 1069 Å² buried · 35 hydrogen bonds · protein-protein
A–B · 1004 Å² buried · 31 hydrogen bonds · protein-protein
A–D · 87 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5H00 · The crystal structure of D-2-haloacid dehalogenase · the same entry in another collection · chain D against D, TM-score 1.00
Q52086 · AlphaFold monomer V2.0 prediction for (R)-2-haloacid dehalogenase (Q52086) · a predicted model of the same protein · chain C 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 Q52086
Elsewhere: RCSB PDB 5H00 · PDBe 5H00 · UniProt Q52086

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