MolNFT v1 · #139143 · protein + RNA

Crystal structure of sepcyse-sepcyss in complex with trnacys from methanocaldococcus jannaschii

5X6B · O-phospho-L-seryl-TRNA:CYS-tRNA synthase: “Crystal structure of sepcyse-sepcyss in complex with trnacys from methanocaldococcus jannaschii”. X-ray diffraction, 15 pockets (best druggability 0.85). MolNFT v1 #139143 on GenesisL1: 3D…

PDB: 5X6B
Type: protein + RNA
Length: 1,064 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: O-phospho-L-seryl-TRNA:CYS-tRNA synthase; Uncharacterized protein MJ1481; Trnacys
UniProt: Q58876
Pockets: 15 · best druggability 0.85

Structure

x-ray diffraction · 5 distinct chains · 44% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
I	O-phospho-L-seryl-TRNA:CYS-tRNA synthase	protein	367	41% helix, 17% strand	—
J	O-phospho-L-seryl-TRNA:CYS-tRNA synthase	protein	377	40% helix, 16% strand	—
E	Uncharacterized protein MJ1481	protein	68	68% helix, 6% strand	Q58876
F	Uncharacterized protein MJ1481	protein	177	51% helix, 10% strand	Q58876
P	Trnacys	rna	75	—	—

Pockets

15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1144	0.85	0.86	101	empty
2	624	0.81	0.86	51	empty
3	865	0.75	0.78	94	empty
4	73	0.74	0.98	23	empty
5	285	0.63	0.81	27	empty

Interfaces

9 interfaces between chains.

I–J · 4021 Å² buried · 57 hydrogen bonds · protein-protein
E–F · 1852 Å² buried · 13 hydrogen bonds · protein-protein
I–P · 1116 Å² buried · 28 hydrogen bonds · protein-nucleic
F–P · 1038 Å² buried · 20 hydrogen bonds · protein-nucleic
J–F · 845 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (cofactor).

Compared structures

5X6B · Crystal structure of SepCysE-SepCysS in complex with tRNACys from Methanocaldococcus… · the same entry in another collection · chain J against J, TM-score 1.00
Q58876 · AlphaFold monomer V2.0 prediction for uncharacterized protein MJ1481 (Q58876) · a predicted model of the same protein · chain E against A, TM-score 0.98

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 Q58876
Elsewhere: RCSB PDB 5X6B · PDBe 5X6B · UniProt Q58876

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