Research workbench

Cryoem structure of the ABC transporter nosdfy complexed with nitrous oxide reductase nosz

Analyse Cryoem structure of the ABC transporter nosdfy complexed with nitrous oxide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7QBA
Type: protein
Length: 2,694 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable ABC transporter binding protein nosd; Probable ABC transporter ATP-binding…
EC: 1.7.2.4
UniProt: P19843, P19844, P19845, P19573
Ligands: ATP, MG, CA
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 5 distinct chains · 33% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Probable ABC transporter binding protein nosd	protein	403	6% helix, 31% strand	P19843
B, C	Probable ABC transporter ATP-binding protein nosf	protein	298	34% helix, 20% strand	P19844
D	Probable ABC transporter permease protein nosy	protein	275	75% helix, 0% strand	P19845
E	Probable ABC transporter permease protein nosy	protein	258	78% helix, 0% strand	P19845
H, I	Nitrous-oxide reductase (EC 1.7.2.4)	protein	581	10% helix, 41% strand	P19573

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains B, C
MG · Magnesium ion · metal · 2 copies · chains B, C
CA · Calcium ion · metal · 2 copies · chains H, I

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	928	0.89	0.92	121	MG, ATP
2	581	0.80	0.85	38	empty
3	99	0.77	0.98	32	empty
4	859	0.74	0.78	72	empty
5	67	0.74	0.98	20	empty

Interfaces

11 interfaces between chains.

H–I · 6049 Å² buried · 66 hydrogen bonds · protein-protein
B–C · 1915 Å² buried · 31 hydrogen bonds · protein-protein
A–H · 1875 Å² buried · 21 hydrogen bonds · protein-protein
D–E · 1861 Å² buried · 12 hydrogen bonds · protein-protein
A–E · 1169 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

7QBA · CryoEM structure of the ABC transporter NosDFY complexed with nitrous oxide reductase NosZ · the same entry in another collection · chain I against I, TM-score 1.00
P19573 · AlphaFold monomer V2.0 prediction for nitrous-oxide reductase (P19573) · a predicted model of the same protein · chain H against A, TM-score 1.00
P19845 · AlphaFold monomer V2.0 prediction for probable ABC transporter permease protein nosy… · a predicted model of the same protein · chain E against A, TM-score 0.96
P19843 · AlphaFold monomer V2.0 prediction for probable ABC transporter binding protein nosd… · a predicted model of the same protein · chain A against A, TM-score 0.91
P19844 · AlphaFold monomer V2.0 prediction for probable ABC transporter ATP- binding protein nosf… · a predicted model of the same protein · chain B against A, TM-score 0.90

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 P19843
Every structure of UniProt P19844
Every structure of UniProt P19845
Every structure of UniProt P19573
Elsewhere: RCSB PDB 7QBA · PDBe 7QBA · UniProt P19843 · UniProt P19844 · UniProt P19845 · UniProt P19573

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