MolNFT v1 · #142655 · protein

Crystal structure of methanosarcina mazei PYLRS(Y306A/Y384F) complexed with zlys

6AB8 · Pyrrolysine--tRNA ligase: “Crystal structure of methanosarcina mazei PYLRS(Y306A/Y384F) complexed with zlys”. X-ray diffraction, 4 ligands (9VC, ATP, MG), 2 pockets (best druggability 0.78). MolNFT v1 #142655 on GenesisL1: 3D…

PDB: 6AB8
Type: protein
Length: 264 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyrrolysine--tRNA ligase
EC: 6.1.1.26
UniProt: A0A0F8JXW8
Ligands: 9VC, ATP, MG, K
Pockets: 2 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyrrolysine--tRNA ligase (EC 6.1.1.26)	protein	264	38% helix, 25% strand	A0A0F8JXW8

Ligands and binding sites

9VC · (2S)-2-azanyl-6-(phenylmethoxycarbonylamino)hexanoic acid · ligand · 2 copies · chains A
ATP · Adenosine-5'-triphosphate · ligand · chains A
MG · Magnesium ion · metal · 3 copies · chains A
K · Potassium ion · metal · 2 copies · chains A

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

Pockets

2 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	418	0.78	0.86	55	MG, ATP, 9VC
2	122	0.41	0.75	19	empty

Compared structures

6AB8 · Crystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) complexed with ZLys · 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 A0A0F8JXW8
Elsewhere: RCSB PDB 6AB8 · PDBe 6AB8 · UniProt A0A0F8JXW8

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