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Crystal structure of ligl in complex with NADH from sphingobium sp. strain syk-6

Analyse Crystal structure of ligl in complex with NADH from sphingobium sp. strain syk-6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4YAG
Type: protein
Length: 542 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: C alpha-dehydrogenase
UniProt: C0SUJ9
Ligands: NAI
Pockets: 4 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 54% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	C alpha-dehydrogenase	protein	271	54% helix, 14% strand	C0SUJ9

Ligands and binding sites

NAI · 1,4-dihydronicotinamide adenine dinucleotide · 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	447	0.78	0.86	49	NAI
2	431	0.78	0.86	49	NAI
3	238	0.56	0.78	23	empty
4	51	0.26	0.73	15	empty

Interfaces

1 interface between chains.

A–B · 2480 Å² buried · 29 hydrogen bonds · protein-protein

Compared structures

4YAG · Crystal structure of LigL in complex with NADH from Sphingobium sp. strain SYK-6 · 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
Every structure of UniProt C0SUJ9
Elsewhere: RCSB PDB 4YAG · PDBe 4YAG · UniProt C0SUJ9

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