SMTL ID : 8zgg.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.75 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: 4 residues within 4Å: Chain E: N.212 Chain F: E.74, S.75, P.76 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain E: E.74, S.75, P.76, L.77 Chain F: N.212, K.272 No protein-ligand interaction detected (PLIP)

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

NAG.3: 4 residues within 4Å: Chain A: H.546, E.547, N.548, R.551 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.547, A:N.548, A:R.551, A:R.551 NAG.8: 2 residues within 4Å: Chain B: E.60, N.63 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.63 NAG.9: 4 residues within 4Å: Chain B: H.546, E.547, N.548, R.551 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.547, B:R.551

2 x AKG: 2-OXOGLUTARIC ACID

AKG.4: 8 residues within 4Å: Chain A: Y.656, L.664, H.667, D.669, C.691, H.719, G.721 Ligands: FE2.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.664, A:D.669 Salt bridges: A:H.667 AKG.10: 10 residues within 4Å: Chain B: Y.656, L.664, H.667, D.669, G.690, C.691, H.719, G.721, I.731 Ligands: FE2.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.656, B:R.729 Salt bridges: B:H.667, B:H.719

2 x FE2: FE (II) ION

FE2.5: 4 residues within 4Å: Chain A: H.667, D.669, H.719 Ligands: AKG.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.669, A:D.669, A:H.719 FE2.11: 3 residues within 4Å: Chain B: D.669, H.719 Ligands: AKG.10 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.669, B:D.669, B:H.719

2 x UDP: URIDINE-5'-DIPHOSPHATE

UDP.6: 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.7 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.46, A:W.75 Hydrogen bonds: A:V.80, A:S.113, A:Y.114, A:D.115, A:G.256 Salt bridges: A:H.253, A:K.259, A:K.259 pi-Stacking: A:Y.114 UDP.12: 13 residues within 4Å: Chain B: V.44, T.46, W.75, V.80, A.81, D.112, S.113, Y.114, D.115, H.253, G.256, K.259 Ligands: MN.13 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.114 Hydrogen bonds: B:V.44, B:D.112, B:S.113, B:Y.114, B:G.256 Salt bridges: B:K.259, B:K.259 pi-Stacking: B:W.75, B:W.75

4 x MN: MANGANESE (II) ION

MN.7: 4 residues within 4Å: Chain A: D.112, H.253, N.255 Ligands: UDP.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.112, A:H.253 MN.13: 4 residues within 4Å: Chain B: D.112, D.115, H.253 Ligands: UDP.12 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.115, B:H.253 MN.15: 2 residues within 4Å: Chain E: D.196 Ligands: 660.14 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.196 MN.17: 2 residues within 4Å: Chain F: D.196 Ligands: 660.16 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.196

2 x 660: [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-[[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]methyl]phosphinic acid

660.14: 18 residues within 4Å: Chain E: L.87, A.88, R.89, D.119, Y.154, K.161, W.163, R.167, H.170, V.171, R.175, D.194, D.196, H.263, D.293, I.294, P.322 Ligands: MN.15 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:V.171 Hydrogen bonds: E:L.87, E:R.175, E:R.175, E:H.263, E:S.264, E:D.293 Salt bridges: E:K.161 pi-Cation interactions: E:R.89 660.16: 16 residues within 4Å: Chain F: L.87, A.88, R.89, D.119, Y.154, W.163, H.170, V.171, R.175, D.194, A.195, D.196, H.263, D.293, I.294 Ligands: MN.17 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:V.171 Hydrogen bonds: F:D.119, F:Y.154, F:R.175, F:R.175, F:D.194, F:D.293, F: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: 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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