MolNFT v1 · #111630 · protein

Crystal structure of an ABC transporter solute binding protein (IPR025997) from actinobacillus succinogenes 130Z (ASUC_0499, target efi-511068) with bound D-xylose

4YWH: “Crystal structure of an ABC transporter solute binding protein (IPR025997) from actinobacillus succinogenes…”. X-ray diffraction, 1 ligand (XYP), 1 pocket (best druggability 0.58). MolNFT v1 #111630 on GenesisL1: 3D structure…

PDB: 4YWH
Type: protein
Length: 617 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ABC transporter solute binding protein
EC: 3.6.3.17
UniProt: A6VLM7
Ligands: XYP
Pockets: 1 · best druggability 0.58

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ABC transporter solute binding protein (EC 3.6.3.17)	protein	310	42% helix, 21% strand	A6VLM7
B	ABC transporter solute binding protein (EC 3.6.3.17)	protein	307	45% helix, 22% strand	A6VLM7

Ligands and binding sites

XYP · beta-D-xylopyranose · sugar · 2 copies · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	465	0.58	0.74	41	empty

Interfaces

1 interface between chains.

A–B · 104 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 13 modified (engineered).

Compared structures

4YWH · CRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM… · 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 A6VLM7
Elsewhere: RCSB PDB 4YWH · PDBe 4YWH · UniProt A6VLM7

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