Research workbench

ABC transporter nosdfy, nucleotide-free in gdn, R-domain 2

Analyse ABC transporter nosdfy, nucleotide-free in gdn, R-domain 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7O10
Type: protein
Length: 1,514 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable ABC transporter binding protein nosd; Probable ABC transporter ATP-binding…
UniProt: P19843, P19844, P19845
Ligands: MG
Pockets: 14 · best druggability 0.82

Structure

electron microscopy · 5 distinct chains · 40% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Probable ABC transporter binding protein nosd	protein	402	6% helix, 37% strand	P19843
B	Probable ABC transporter ATP-binding protein nosf	protein	299	31% helix, 15% strand	P19844
C	Probable ABC transporter ATP-binding protein nosf	protein	298	33% helix, 20% strand	P19844
D	Probable ABC transporter permease protein nosy	protein	267	76% helix, 0% strand	P19845
E	Probable ABC transporter permease protein nosy	protein	248	75% helix, 0% strand	P19845

Ligands and binding sites

MG · Magnesium ion · metal · chains A

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

Pockets

14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1156	0.82	0.83	109	empty
2	1104	0.81	0.82	93	empty
3	102	0.76	0.96	25	empty
4	452	0.72	0.82	42	empty
5	80	0.62	0.89	19	empty

Interfaces

7 interfaces between chains.

B–C · 1771 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 1202 Å² buried · 12 hydrogen bonds · protein-protein
B–E · 1154 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 992 Å² buried · 13 hydrogen bonds · protein-protein
A–E · 862 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

7O10 · ABC transporter NosDFY, nucleotide-free in GDN, R-domain 2 · the same entry in another collection · chain E against E, TM-score 1.00
P19844 · AlphaFold monomer V2.0 prediction for probable ABC transporter ATP- binding protein nosf… · a predicted model of the same protein · chain C 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 0.96
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 0.94

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
Elsewhere: RCSB PDB 7O10 · PDBe 7O10 · UniProt P19843 · UniProt P19844 · UniProt P19845

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