MolNFT v1 · #103135 · protein

Crystal structure of S. typhimurium peptidyl-tRNA hydrolase

4P7B: “Crystal structure of S. typhimurium peptidyl-tRNA hydrolase”. X-ray diffraction, 5 pockets (best druggability 0.67). MolNFT v1 #103135 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4P7B
Type: protein
Length: 381 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptidyl-tRNA hydrolase
EC: 3.1.1.29
UniProt: D0ZJ57
Pockets: 5 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptidyl-tRNA hydrolase (EC 3.1.1.29)	protein	188	44% helix, 21% strand	D0ZJ57
C	Peptidyl-tRNA hydrolase (EC 3.1.1.29)	protein	193	45% helix, 21% strand	D0ZJ57

Ligands and binding sites

TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	275	0.67	0.83	37	empty
2	98	0.38	0.76	24	empty
3	56	0.34	0.78	21	empty
4	62	0.30	0.74	14	TRS
5	64	0.30	0.74	14	TRS

Interfaces

1 interface between chains.

A–C · 413 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

4P7B · Crystal structure of S. typhimurium peptidyl-tRNA hydrolase · 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 D0ZJ57
Elsewhere: RCSB PDB 4P7B · PDBe 4P7B · UniProt D0ZJ57

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