MolNFT v1 · #24964 · protein

Escherichia COLI tyrosyl-tRNA synthetase mutant complexed with tyr-ams

1VBN: “Escherichia COLI tyrosyl-tRNA synthetase mutant complexed with tyr-ams”. X-ray diffraction, 1 ligand (YSA), 5 pockets (best druggability 0.74). MolNFT v1 #24964 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1VBN
Type: protein
Length: 636 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tyrosyl-tRNA synthetase
EC: 6.1.1.1
UniProt: P00951
Ligands: YSA
Pockets: 5 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 53% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Tyrosyl-tRNA synthetase (EC 6.1.1.1)	protein	318	53% helix, 10% strand	P00951

Ligands and binding sites

YSA · 5'-O-[N-(L-tyrosyl)sulfamoyl]adenosine · ligand · 2 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	499	0.74	0.83	60	YSA
2	373	0.71	0.83	54	YSA
3	51	0.60	0.92	20	empty
4	75	0.34	0.76	14	empty
5	68	0.32	0.75	14	empty

Interfaces

1 interface between chains.

A–B · 1595 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

1VBN · Escherichia coli tyrosyl-tRNA synthetase mutant complexed with Tyr-AMS · the same entry in another collection · chain B against B, 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 P00951
Elsewhere: RCSB PDB 1VBN · PDBe 1VBN · UniProt P00951

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