SMTL ID : 8zgh.1

Human lysine O-link glycosylation complex, LH3/ColGalT1 in its apo state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.93 Å

Oligo State

hetero-4-4-mer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG.1: 3 residues within 4Å: Chain E: N.212 Chain F: E.74, S.75 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain E: E.74, S.75 Chain F: N.212, K.272 No protein-ligand interaction detected (PLIP)

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose

NAG.3: 3 residues within 4Å: Chain A: H.546, N.548, R.551 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.551 NAG.6: 2 residues within 4Å: Chain B: N.63, T.65 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.65 NAG.7: 3 residues within 4Å: Chain B: H.546, N.548, R.551 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.551, B:R.551

2 x AKG: 2-OXOGLUTARIC ACID

AKG.4: 9 residues within 4Å: Chain A: V.607, T.609, Y.656, L.664, H.667, D.669, H.719, F.735 Ligands: FE2.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.664, A:F.735 Hydrogen bonds: A:T.609 Salt bridges: A:H.667, A:H.667, A:H.719 AKG.8: 7 residues within 4Å: Chain B: V.607, T.609, L.664, H.667, D.669, H.719 Ligands: FE2.9 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.664 Hydrogen bonds: B:T.609, B:Y.656 Salt bridges: B:H.667, B:H.719

2 x FE2: FE (II) ION

FE2.5: 5 residues within 4Å: Chain A: D.669, T.674, H.719, F.735 Ligands: AKG.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.669, A:D.669 FE2.9: 5 residues within 4Å: Chain B: D.669, T.674, H.711, H.719 Ligands: AKG.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.669, B:H.719

2 x GDU: GALACTOSE-URIDINE-5'-DIPHOSPHATE

GDU.10: 16 residues within 4Å: Chain E: L.87, A.88, R.89, Y.154, K.161, W.163, H.170, V.171, R.175, D.194, D.196, H.263, D.293, I.294, P.322 Ligands: MN.11 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:V.171 Hydrogen bonds: E:L.87, E:R.89, E:R.89, E:R.175, E:R.175 Salt bridges: E:K.161 GDU.12: 15 residues within 4Å: Chain F: L.87, A.88, R.89, Y.154, W.163, R.167, V.171, R.175, D.194, A.195, D.196, D.293, I.294, P.322 Ligands: MN.13 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:V.171 Hydrogen bonds: F:L.87, F:R.89, F:Y.154, F:R.175, F:R.175, F:D.194, F:D.194, F:A.195, F:D.293

2 x MN: MANGANESE (II) ION

MN.11: 2 residues within 4Å: Chain E: D.196 Ligands: GDU.10 No protein-ligand interaction detected (PLIP) MN.13: 2 residues within 4Å: Chain F: D.196 Ligands: GDU.12 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.196, F:D.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Peng, J. et al., The structural basis for the human procollagen lysine hydroxylation and dual-glycosylation. Nat Commun (2025)

Release Date

2025-03-19

Peptides

Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3: ABCD
Procollagen galactosyltransferase 1: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
U

F
V

G
W

H
X

Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3

Procollagen galactosyltransferase 1

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