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L-2-chlorobutryic acid bound complex L-haloacid dehalogenase from a rhodobacteraceae family bacterium

Analyse L-2-chlorobutryic acid bound complex L-haloacid dehalogenase from a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2YN4
Type: protein
Length: 450 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-haloacid dehalogenase
Ligands: 39J
Pockets: 4 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	L-haloacid dehalogenase	protein	225	48% helix, 13% strand	—

Ligands and binding sites

39J · (2S)-2-chlorobutanoic acid · ligand · 2 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	179	0.55	0.80	32	empty
2	213	0.54	0.78	31	empty
3	91	0.47	0.81	22	empty
4	56	0.34	0.78	14	empty

Interfaces

1 interface between chains.

A–B · 1919 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

2YN4 · L-2-chlorobutryic acid bound complex L-haloacid dehalogenase from a Rhodobacteraceae… · 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
Elsewhere: RCSB PDB 2YN4 · PDBe 2YN4

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