MolNFT v1 · #159722 · protein

Crystal structure of mray bound to 3'-hydroxymureidomycin a

6OZ6 · Mrayaa nanobody: “Crystal structure of mray bound to 3'-hydroxymureidomycin a”. X-ray diffraction, 1 ligand (NKD), 20 pockets (best druggability 0.83). MolNFT v1 #159722 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6OZ6
Type: protein
Length: 1,764 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mrayaa nanobody; Phospho-N-acetylmuramoyl-pentapeptide-transferase
EC: 2.7.8.13
UniProt: O66465
Ligands: NKD
Pockets: 20 · best druggability 0.83

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, F, G	Mrayaa nanobody	protein	126	7% helix, 49% strand	—
A	Phospho-N-acetylmuramoyl-pentapeptide-transferase (EC 2.7.8.13)	protein	331	72% helix, 2% strand	O66465
B	Phospho-N-acetylmuramoyl-pentapeptide-transferase (EC 2.7.8.13)	protein	321	73% helix, 2% strand	O66465
C	Phospho-N-acetylmuramoyl-pentapeptide-transferase (EC 2.7.8.13)	protein	322	70% helix, 2% strand	O66465
H	Mrayaa nanobody	protein	124	7% helix, 50% strand	—
D	Phospho-N-acetylmuramoyl-pentapeptide-transferase (EC 2.7.8.13)	protein	288	76% helix, 2% strand	O66465

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	999	0.83	0.84	62	empty
2	1047	0.81	0.81	72	empty
3	122	0.70	0.91	31	empty
4	107	0.69	0.92	33	empty
5	365	0.67	0.80	61	empty

Interfaces

7 interfaces between chains.

A–B · 1513 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1351 Å² buried · 16 hydrogen bonds · protein-protein
G–C · 647 Å² buried · 8 hydrogen bonds · protein-protein
E–A · 636 Å² buried · 6 hydrogen bonds · protein-protein
F–B · 602 Å² 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

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