SMTL ID : 7zvj.1

Homodimeric structure of LARGE1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

homo-dimer

Ligands

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 4 residues within 4Å: Chain A: N.15, Q.385, M.391 Ligands: PO4.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.15, A:R.18, A:R.18, A:Q.385 NAG.4: 5 residues within 4Å: Chain B: N.15, R.18, Q.385, M.391 Ligands: PO4.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.18, B:Q.385

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 5 residues within 4Å: Chain A: G.13, Y.14, N.15, H.329 Ligands: NAG.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.14, A:N.15, A:N.15 Salt bridges: A:H.329 PO4.5: 5 residues within 4Å: Chain B: G.13, Y.14, N.15, H.329 Ligands: NAG.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.14, B:N.15, B:N.15, B:N.15 Salt bridges: B:H.329 PO4.6: 3 residues within 4Å: Chain A: R.468 Chain B: R.468, R.470 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.468, B:R.470, A:R.468

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 3 residues within 4Å: Chain A: D.432, H.572, H.575 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.432 MN.7: 3 residues within 4Å: Chain B: D.432, H.572, H.575 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Katz, M. et al., Structural basis for matriglycan synthesis by the LARGE1 dual glycosyltransferase. Plos One (2022)

Release Date

2022-11-30

Peptides

Xylosyl- and glucuronyltransferase LARGE1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Xylosyl- and glucuronyltransferase LARGE1