MolNFT v1 · #120423 · protein

The complex structure of D-2-haloacid dehalogenase with L-la

5GZY · (R)-2-haloacid dehalogenase: “The complex structure of D-2-haloacid dehalogenase with L-la”. X-ray diffraction, 1 ligand (2OP), 10 pockets (best druggability 0.73). MolNFT v1 #120423 on GenesisL1: 3D structure, binding sites and…

PDB: 5GZY
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
Ligands: 2OP
Pockets: 10 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 66% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	(R)-2-haloacid dehalogenase (EC 3.8.1.9)	protein	293	66% helix, 1% strand	Q52086
B, C	(R)-2-haloacid dehalogenase (EC 3.8.1.9)	protein	291	66% helix, 1% strand	Q52086

Ligands and binding sites

2OP · (2S)-2-hydroxypropanoic acid · ligand · 4 copies · chains A, B, C, D

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

Pockets

10 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	804	0.73	0.78	91	empty
2	541	0.67	0.78	58	empty
3	397	0.62	0.77	36	empty
4	143	0.54	0.81	27	empty
5	82	0.53	0.85	17	empty

Interfaces

6 interfaces between chains.

C–D · 1164 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1134 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 1043 Å² buried · 42 hydrogen bonds · protein-protein
B–C · 1037 Å² buried · 31 hydrogen bonds · protein-protein
A–C · 103 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5GZY · The complex structure of D-2-haloacid dehalogenase with L-LA · 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 B 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 5GZY · PDBe 5GZY · UniProt Q52086

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