SMTL ID : 9e1t.1

CryoEM structure of LARGE1 bound to UDP-GlcA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: D.573, H.713, H.716 Ligands: UGA.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.573, A:H.713, A:H.716 MN.3: 4 residues within 4Å: Chain B: D.573, H.713, H.716 Ligands: UGA.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.573, B:H.713, B:H.716

2 x UGA: URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID(Non-covalent)

UGA.2: 22 residues within 4Å: Chain A: Q.487, L.488, S.489, D.491, R.492, Y.549, D.571, I.572, D.573, F.633, E.666, Y.668, F.685, G.686, W.687, N.688, K.689, H.716, S.719, D.721, I.722 Ligands: MN.1 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Q.487, A:D.571, A:D.571, A:I.572, A:G.686, A:N.688, A:N.688, A:S.719, A:S.719, A:D.721, A:D.721 Salt bridges: A:R.492, A:H.716 pi-Stacking: A:Y.549 UGA.4: 21 residues within 4Å: Chain B: Q.487, L.488, S.489, D.491, R.492, Y.549, D.571, I.572, D.573, R.634, E.666, Y.668, F.685, G.686, W.687, N.688, K.689, H.716, S.719, D.721 Ligands: MN.3 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:Q.487, B:R.492, B:D.571, B:D.571, B:I.572, B:D.573, B:Y.668, B:G.686, B:G.686, B:N.688, B:K.689, B:S.719, B:D.721, B:D.721 Salt bridges: B:K.689, B:H.716 pi-Stacking: B:Y.549

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joseph, S. et al., LARGE1 processively polymerizes length-controlled matriglycan on prodystroglycan. Nat Commun (2025)

Release Date

2025-02-12

Peptides

Xylosyl- and glucuronyltransferase LARGE1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Xylosyl- and glucuronyltransferase LARGE1

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