MolNFT v1 · #117503 · protein

Crystal structure of holo NAD(P)H dehydrogenase, quinone 1

5EA2 · NAD(P)H dehydrogenase [quinone] 1: “Crystal structure of holo NAD(P)H dehydrogenase, quinone 1”. X-ray diffraction, 1 ligand (FAD), 10 pockets (best druggability 0.85). MolNFT v1 #117503 on GenesisL1: 3D structure, binding sites and…

PDB: 5EA2
Type: protein
Length: 1,090 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NAD(P)H dehydrogenase [quinone] 1
EC: 1.6.5.2
UniProt: P15559
Ligands: FAD
Pockets: 10 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 39% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NAD(P)H dehydrogenase [quinone] 1 (EC 1.6.5.2)	protein	273	40% helix, 16% strand	P15559
C	NAD(P)H dehydrogenase [quinone] 1 (EC 1.6.5.2)	protein	276	39% helix, 16% strand	P15559
E	NAD(P)H dehydrogenase [quinone] 1 (EC 1.6.5.2)	protein	270	40% helix, 16% strand	P15559
G	NAD(P)H dehydrogenase [quinone] 1 (EC 1.6.5.2)	protein	271	38% helix, 16% strand	P15559

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, C, E, G

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

Pockets

10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1190	0.85	0.86	112	empty
2	92	0.78	0.99	18	empty
3	82	0.77	0.99	18	empty
4	586	0.77	0.83	47	FAD
5	579	0.76	0.82	47	FAD

Interfaces

5 interfaces between chains.

A–C · 2883 Å² buried · 41 hydrogen bonds · protein-protein
E–G · 2870 Å² buried · 33 hydrogen bonds · protein-protein
A–E · 449 Å² buried · 6 hydrogen bonds · protein-protein
C–G · 415 Å² buried · 6 hydrogen bonds · protein-protein
A–G · 95 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5EA2 · Crystal Structure of Holo NAD(P)H dehydrogenase, qui 1 · the same entry in another collection · chain G against G, TM-score 1.00
P15559 · AlphaFold monomer V2.0 prediction for NAD(P)H dehydrogenase [quinone] 1 (P15559) · a predicted model of the same protein · chain E 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 P15559
Elsewhere: RCSB PDB 5EA2 · PDBe 5EA2 · UniProt P15559

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