MolNFT v1 · #141821 · protein

Crystal structure of rimk complexed with rpsf

5ZK6 · Ribosomal protein S6--L-glutamate ligase: “Crystal structure of rimk complexed with rpsf”. X-ray diffraction, 2 ligands (ADP, MG), 1 pocket (best druggability 0.76). MolNFT v1 #141821 on GenesisL1: 3D structure, binding sites and…

PDB: 5ZK6
Type: protein
Length: 291 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribosomal protein S6--L-glutamate ligase
EC: 6.3.2.-
UniProt: P0C0U4
Ligands: ADP, MG
Pockets: 1 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribosomal protein S6--L-glutamate ligase (EC 6.3.2.-)	protein	291	34% helix, 30% strand	P0C0U4

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A
MG · Magnesium ion · metal · chains A

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	631	0.76	0.82	69	ADP, MG

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

5ZK6 · Crystal structure of RimK complexed with RpsF · the same entry in another collection · chain A against A, TM-score 1.00
P0C0U4 · AlphaFold monomer V2.0 prediction for ribosomal protein S6-- L-glutamate ligase (P0C0U4) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P0C0U4
Elsewhere: RCSB PDB 5ZK6 · PDBe 5ZK6 · UniProt P0C0U4

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