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Structure of bacterial type II NADH dehydrogenase from caldalkalibacillus thermarum at 2.5A resolution

Analyse Structure of bacterial type II NADH dehydrogenase from caldalkalibacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4NWZ
Type: protein
Length: 1,557 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: FAD-dependent pyridine nucleotide-disulfide oxidoreductase
UniProt: F5L3B8
Ligands: FAD
Pockets: 15 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 36% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	FAD-dependent pyridine nucleotide-disulfide oxidoreductase	protein	395	35% helix, 27% strand	F5L3B8
C	FAD-dependent pyridine nucleotide-disulfide oxidoreductase	protein	394	35% helix, 27% strand	F5L3B8
D	FAD-dependent pyridine nucleotide-disulfide oxidoreductase	protein	373	37% helix, 23% strand	F5L3B8

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D

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

Pockets

15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1052	0.82	0.83	115	FAD
2	903	0.82	0.84	88	FAD
3	429	0.80	0.88	67	empty
4	435	0.80	0.88	52	FAD
5	403	0.78	0.87	57	FAD

Interfaces

5 interfaces between chains.

B–C · 660 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 354 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 279 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 215 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 202 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4NWZ · Structure of bacterial type II NADH dehydrogenase from Caldalkalibacillus thermarum at… · the same entry in another collection · chain D against D, 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 F5L3B8
Elsewhere: RCSB PDB 4NWZ · PDBe 4NWZ · UniProt F5L3B8

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