MolNFT v1 · #111301 · protein

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

4YMU · ABC-type polar amino acid transport system, ATPase component: “Crystal structure of an amino acid ABC transporter complex with arginines and atps”. X-ray diffraction, 3 ligands (ATP, ARG, MG), 12 pockets (best druggability 0.71).…

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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