Crystal structure of mray bound to 3'-hydroxymureidomycin a

Structure

x-ray diffraction · 6 distinct chains · 62% helix, 10% strand (DSSP).

Ligands and binding sites

• NKD · (2~{S})-2-[[(2~{S})-1-[[(2~{S},3~{S})-3-[[(2~{S})-2-azanyl-3-(3-hydroxyphenyl)propanoyl]-methyl-amino]-1-[[(~{Z})-[(3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl) oxolan-2-ylidene]methyl]amino]-1-oxidanylidene-butan-2-yl]amino]-4-methylsulfanyl-1-oxidanylidene-butan-2-yl]carbamoylamino]-3-(3-hydroxyphenyl)propanoic acid · ligand · 3 copies · chains A, B, C

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

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Interfaces

7 interfaces between chains.

• A–B · 1513 Ų buried · 18 hydrogen bonds · protein-protein
• C–D · 1351 Ų buried · 16 hydrogen bonds · protein-protein
• G–C · 647 Ų buried · 8 hydrogen bonds · protein-protein
• E–A · 636 Ų buried · 6 hydrogen bonds · protein-protein
• F–B · 602 Ų buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

• 6OZ6 · Crystal structure of MraY bound to 3'-hydroxymureidomycin A · the same entry in another collection · chain D against D, TM-score 1.00
• O66465 · AlphaFold monomer V2.0 prediction for phospho-N-acetylmuramoyl- pentapeptide-transferase… · a predicted model of the same protein · chain D against A, TM-score 0.99

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 O66465
• Elsewhere: RCSB PDB 6OZ6 · PDBe 6OZ6 · UniProt O66465