SMTL ID : 8zge.1

Human lysine O-link glycosylation complex, LH3/ColGalT1 tetramer with bound UDP-galactose

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-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: 5 residues within 4Å: Chain C: N.212, K.272 Chain D: E.74, S.75, L.77 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain C: E.74, S.75, L.77 Chain D: N.212, K.272 No protein-ligand interaction detected (PLIP)

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

NAG.3: 1 residues within 4Å: Chain A: N.63 No protein-ligand interaction detected (PLIP) NAG.4: 4 residues within 4Å: Chain A: H.546, E.547, N.548, R.551 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.547, A:R.551, A:R.551 NAG.9: 1 residues within 4Å: Chain B: N.63 No protein-ligand interaction detected (PLIP) NAG.10: 4 residues within 4Å: Chain B: H.546, E.547, N.548, R.551 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.547, B:E.547, B:R.551, B:R.551

2 x AKG: 2-OXOGLUTARIC ACID

AKG.5: 9 residues within 4Å: Chain A: Y.656, H.667, D.669, G.690, C.691, H.719, G.721, F.735 Ligands: FE2.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.656, A:Y.656 Salt bridges: A:H.667, A:R.729 AKG.11: 9 residues within 4Å: Chain B: Y.656, L.664, H.667, D.669, N.676, C.691, H.719, F.735 Ligands: FE2.12 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.656, B:Y.656, B:N.676 Salt bridges: B:H.667, B:R.729

2 x FE2: FE (II) ION

FE2.6: 5 residues within 4Å: Chain A: H.667, D.669, H.719, F.735 Ligands: AKG.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.669, A:D.669, A:H.719 FE2.12: 5 residues within 4Å: Chain B: H.667, D.669, H.719, F.735 Ligands: AKG.11 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.669, B:D.669, B:H.719

4 x UDP: URIDINE-5'-DIPHOSPHATE

UDP.7: 15 residues within 4Å: Chain A: V.44, T.46, W.75, V.80, A.81, K.89, D.112, S.113, Y.114, D.115, H.253, N.255, G.256, K.259 Ligands: MN.8 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:T.46 Hydrogen bonds: A:S.113, A:Y.114, A:D.115, A:G.256 Salt bridges: A:K.259, A:K.259 pi-Stacking: A:W.75, A:W.75, A:Y.114 UDP.13: 15 residues within 4Å: Chain B: V.44, T.46, W.75, V.80, A.81, K.89, D.112, S.113, Y.114, D.115, H.253, N.255, G.256, K.259 Ligands: MN.14 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:T.46 Hydrogen bonds: B:D.112, B:S.113, B:Y.114, B:D.115, B:G.256 Salt bridges: B:K.259, B:K.259 pi-Stacking: B:W.75, B:W.75, B:Y.114 UDP.16: 18 residues within 4Å: Chain C: I.374, L.376, R.382, A.402, V.403, D.404, G.405, G.436, C.440, S.443, E.463, D.465, Y.595, V.596, S.597, D.598, T.599 Ligands: MN.18 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:L.376, C:A.402 Hydrogen bonds: C:I.374, C:G.405, C:S.443, C:S.443, C:S.597, C:D.598, C:D.598 Salt bridges: C:R.382 UDP.20: 18 residues within 4Å: Chain D: I.374, L.376, R.382, A.402, V.403, D.404, G.405, G.436, C.440, S.443, E.463, D.465, Y.595, V.596, S.597, D.598, T.599 Ligands: MN.22 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:L.376, D:A.402 Hydrogen bonds: D:I.374, D:G.405, D:S.443, D:S.443, D:S.597, D:D.598, D:D.598 Salt bridges: D:R.382

6 x MN: MANGANESE (II) ION

MN.8: 4 residues within 4Å: Chain A: D.112, D.115, H.253 Ligands: UDP.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.115, A:D.115, A:H.253 MN.14: 4 residues within 4Å: Chain B: D.112, D.115, H.253 Ligands: UDP.13 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.115, B:D.115, B:H.253 MN.17: 3 residues within 4Å: Chain C: D.196, P.320 Ligands: GDU.15 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.196 MN.18: 3 residues within 4Å: Chain C: R.382, D.465 Ligands: UDP.16 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.465 MN.21: 3 residues within 4Å: Chain D: D.196, P.320 Ligands: GDU.19 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.196 MN.22: 3 residues within 4Å: Chain D: R.382, D.465 Ligands: UDP.20 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.465

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

GDU.15: 18 residues within 4Å: Chain C: L.87, A.88, R.89, D.119, Y.154, W.163, R.167, H.170, R.175, D.194, A.195, D.196, S.264, D.292, D.293, I.294, P.322 Ligands: MN.17 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:R.89 Hydrogen bonds: C:R.89, C:R.89, C:R.167, C:R.175, C:R.175, C:A.195, C:S.264, C:D.292, C:D.293 GDU.19: 18 residues within 4Å: Chain D: L.87, A.88, R.89, D.119, Y.154, W.163, R.167, H.170, R.175, D.194, A.195, D.196, S.264, D.292, D.293, I.294, P.322 Ligands: MN.21 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:R.89 Hydrogen bonds: D:R.89, D:R.89, D:Y.154, D:R.167, D:R.175, D:R.175, D:A.195, D:S.264, D:D.292, D:D.293

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: AB
Procollagen galactosyltransferase 1: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
U

D
V

Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3

Procollagen galactosyltransferase 1

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