MolNFT v1 · #106410 · protein

Crystal structure of ABC transporter solute binding protein AVI_3567 from agrobacterium vitis S4, target efi-510645, with bound D-mannitol

4RYA · ABC transporter substrate binding protein (sorbitol): “Crystal structure of ABC transporter solute binding protein AVI_3567 from agrobacterium vitis S4, target…”. X-ray diffraction, 1 ligand (MTL), 3 pockets (best druggability…

PDB: 4RYA
Type: protein
Length: 417 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ABC transporter substrate binding protein (sorbitol)
UniProt: B9JRF8
Ligands: MTL
Pockets: 3 · best druggability 0.48

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ABC transporter substrate binding protein (sorbitol)	protein	417	47% helix, 16% strand	B9JRF8

Ligands and binding sites

MTL · D-mannitol · ligand · chains A
ACT · Acetate ion · additive · chains A

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	157	0.48	0.77	26	empty
2	53	0.32	0.77	17	empty
3	68	0.29	0.73	16	empty

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

4RYA · Crystal structure of abc transporter solute binding protein AVI_3567 from AGROBACTERIUM… · the same entry in another collection · chain A against A, 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 B9JRF8
Elsewhere: RCSB PDB 4RYA · PDBe 4RYA · UniProt B9JRF8

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