MolNFT v1 · #8817 · protein

Prolyl-tRNA synthetase from thermus thermophilus

1HC7: “Prolyl-tRNA synthetase from thermus thermophilus”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.84). MolNFT v1 #8817 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1HC7
Type: protein
Length: 1,856 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Prolyl-tRNA synthetase
EC: 6.1.1.15
Ligands: ZN
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Prolyl-tRNA synthetase (EC 6.1.1.15)	protein	464	36% helix, 28% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1197	0.84	0.85	109	empty
2	768	0.81	0.85	62	empty
3	848	0.78	0.81	72	empty
4	590	0.71	0.79	45	empty
5	669	0.69	0.77	54	empty

Interfaces

3 interfaces between chains.

A–B · 2479 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 2385 Å² buried · 28 hydrogen bonds · protein-protein
B–D · 1099 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

1HC7 · Prolyl-tRNA synthetase from Thermus thermophilus · 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
Elsewhere: RCSB PDB 1HC7 · PDBe 1HC7

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