Research workbench

ABC transporter complex nosdfyl, R-domain 3

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

PDB: 7OSI
Type: protein
Length: 1,665 residues
Chains: 6
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, Q52529
Ligands: MG, CU, ZN
Pockets: 13 · best druggability 0.81

Structure

electron microscopy · 6 distinct chains · 39% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Probable ABC transporter binding protein nosd	protein	392	7% helix, 35% strand	P19843
B	Probable ABC transporter ATP-binding protein nosf	protein	308	33% helix, 21% strand	P19844
C	Probable ABC transporter ATP-binding protein nosf	protein	307	31% 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	77% helix, 0% strand	P19845
H	Copper-binding lipoprotein nosl	protein	143	21% helix, 12% strand	Q52529

Ligands and binding sites

MG · Magnesium ion · metal · chains A
CU · Copper (II) ion · metal · chains A, H
ZN · Zinc ion · metal · chains H

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

Pockets

13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	995	0.81	0.83	106	empty
2	1030	0.81	0.81	85	empty
3	415	0.73	0.83	44	empty
4	77	0.73	0.96	22	empty
5	456	0.64	0.77	51	empty

Interfaces

9 interfaces between chains.

B–C · 2335 Å² buried · 25 hydrogen bonds · protein-protein
A–H · 1168 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 1151 Å² buried · 10 hydrogen bonds · protein-protein
B–E · 1132 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 944 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

7OSI · ABC Transporter complex NosDFYL, R-domain 3 · the same entry in another collection · chain H against H, TM-score 1.00
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
Q52529 · AlphaFold monomer V2.0 prediction for copper-binding lipoprotein nosl (Q52529) · a predicted model of the same protein · chain H 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 0.95
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 0.95

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 Q52529
Elsewhere: RCSB PDB 7OSI · PDBe 7OSI · UniProt P19843 · UniProt P19844 · UniProt P19845 · UniProt Q52529

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