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Sulfate bound L-haloacid dehalogenase from a rhodobacteraceae family bacterium

Analyse Sulfate bound L-haloacid dehalogenase from a rhodobacteraceae family bacterium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2YMM
Type: protein
Length: 903 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-haloacid dehalogenase
Ligands: SO4
Pockets: 10 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	L-haloacid dehalogenase	protein	225	48% helix, 13% strand	—
B	L-haloacid dehalogenase	protein	228	47% helix, 13% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 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	51	0.70	0.98	20	empty
2	205	0.59	0.81	32	empty
3	204	0.59	0.81	31	empty
4	199	0.58	0.80	31	empty
5	191	0.57	0.80	29	empty

Interfaces

2 interfaces between chains.

C–D · 1922 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1920 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

2YMM · Sulfate bound L-haloacid dehalogenase from a Rhodobacteraceae family bacterium · 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 2YMM · PDBe 2YMM

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