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Crystal structure of an amino acid ABC transporter complex with arginines and atps

Analyse Crystal structure of an amino acid ABC transporter complex with arginines and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4YMU
Type: protein
Length: 909 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ABC-type polar amino acid transport system, ATPase component; ABC-type amino acid…
UniProt: Q8RCC2, Q8RCC3
Ligands: ATP, ARG, MG
Pockets: 12 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 67% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
J, A	ABC-type polar amino acid transport system, ATPase component	protein	240	43% helix, 25% strand	Q8RCC2
D	ABC-type amino acid transport system, permease component	protein	215	80% helix, 0% strand	Q8RCC3
C	ABC-type amino acid transport system, permease component	protein	214	82% helix, 0% strand	Q8RCC3

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains J, A
ARG · Arginine · ligand · 2 copies · chains D, C
MG · Magnesium ion · metal · 2 copies · chains J, A

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

Pockets

12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	542	0.71	0.80	57	ARG
2	588	0.66	0.76	53	empty
3	83	0.35	0.75	16	empty
4	84	0.35	0.74	17	empty
5	103	0.34	0.73	22	ATP, MG

Interfaces

4 interfaces between chains.

D–C · 1630 Å² buried · 20 hydrogen bonds · protein-protein
J–C · 872 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 871 Å² buried · 10 hydrogen bonds · protein-protein
J–A · 580 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4YMU · Crystal structure of an amino acid ABC transporter complex with arginines and ATPs · the same entry in another collection · chain J against J, 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 Q8RCC2
Every structure of UniProt Q8RCC3
Elsewhere: RCSB PDB 4YMU · PDBe 4YMU · UniProt Q8RCC2 · UniProt Q8RCC3

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