MolNFT v1 · #161415 · protein

Structure of E.COLI rlmj in complex with a bisubstrate analogue (BA4)

6QDX · Ribosomal RNA large subunit methyltransferase J: “Structure of E.COLI rlmj in complex with a bisubstrate analogue (BA4)”. X-ray diffraction, 1 ligand (HY8), 13 pockets (best druggability 0.71). MolNFT v1 #161415 on GenesisL1: 3D…

PDB: 6QDX
Type: protein
Length: 1,092 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribosomal RNA large subunit methyltransferase J
EC: 2.1.1.266
UniProt: A0A0G3KF30
Ligands: HY8
Pockets: 13 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribosomal RNA large subunit methyltransferase J (EC 2.1.1.266)	protein	273	37% helix, 21% strand	A0A0G3KF30
B, C, D	Ribosomal RNA large subunit methyltransferase J (EC 2.1.1.266)	protein	273	37% helix, 20% strand	A0A0G3KF30

Ligands and binding sites

HY8 · (2~{S})-4-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[3-[[9-[(2~{S},3~{R},4~{S},5~{S})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-6-yl]amino]propyl]amino]-2-azanyl-butanoic acid · ligand · 4 copies · chains A, B, C, D

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

Pockets

13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	501	0.71	0.81	63	empty
2	632	0.71	0.79	58	empty
3	585	0.63	0.75	55	empty
4	392	0.62	0.77	41	HY8
5	362	0.61	0.78	40	HY8

Interfaces

5 interfaces between chains.

B–C · 615 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 555 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 334 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 267 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 213 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6QDX · Structure of E.coli RlmJ in complex with a bisubstrate analogue (BA4) · 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 A0A0G3KF30
Elsewhere: RCSB PDB 6QDX · PDBe 6QDX · UniProt A0A0G3KF30

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