Research workbench

Crystal structure of mray in complex with muraymycin D2

Analyse Crystal structure of mray in complex with muraymycin D2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5CKR
Type: protein
Length: 329 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phospho-N-acetylmuramoyl-pentapeptide-transferase
EC: 2.7.8.13
UniProt: O66465
Ligands: 57M
Pockets: 3 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 73% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phospho-N-acetylmuramoyl-pentapeptide-transferase (EC 2.7.8.13)	protein	329	73% helix, 2% strand	O66465

Ligands and binding sites

57M · Muraymycin D2 · ligand · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	67	0.58	0.89	22	empty
2	140	0.52	0.79	24	empty
3	116	0.37	0.74	23	57M

Compared structures

5CKR · Crystal Structure of MraY in complex with Muraymycin D2 · the same entry in another collection · chain A against A, TM-score 1.00
O66465 · AlphaFold monomer V2.0 prediction for phospho-N-acetylmuramoyl- pentapeptide-transferase… · a predicted model of the same protein · chain A against A, TM-score 0.98

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 5CKR · PDBe 5CKR · UniProt O66465

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.