SMTL ID : 8zgc.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.58 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 C: N.212 Chain D: E.74, S.75 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain C: E.74, S.75 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.63 NAG.4: 4 residues within 4Å: Chain A: H.546, E.547, N.548, R.551 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.548, A:R.551 NAG.9: 2 residues within 4Å: Chain B: E.60, N.63 No protein-ligand interaction detected (PLIP) NAG.10: 4 residues within 4Å: Chain B: H.546, E.547, N.548, R.551 No protein-ligand interaction detected (PLIP)

2 x AKG: 2-OXOGLUTARIC ACID

AKG.5: 8 residues within 4Å: Chain A: F.652, L.664, H.667, N.676, H.719, V.733, F.735 Ligands: FE2.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.733, A:F.735 Salt bridges: A:H.667, A:H.719 AKG.11: 8 residues within 4Å: Chain B: T.609, F.652, Y.656, L.664, H.667, H.719, I.731 Ligands: FE2.12 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.652, B:L.664 Hydrogen bonds: B:T.609, B:T.609, B:Y.656 Salt bridges: B:H.667

2 x FE2: FE (II) ION

FE2.6: 4 residues within 4Å: Chain A: H.667, D.669, H.719 Ligands: AKG.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.669, A:D.669, A:H.719 FE2.12: 4 residues within 4Å: Chain B: H.667, D.669, H.719 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: 12 residues within 4Å: Chain A: V.44, T.46, W.75, V.80, A.81, K.89, D.112, Y.114, H.253, N.255, G.256 Ligands: MN.8 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.46, A:W.75, A:Y.114 Hydrogen bonds: A:V.80, A:K.89, A:G.256 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 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:T.46 Hydrogen bonds: B:V.44, B:T.46, 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: 16 residues within 4Å: Chain C: I.374, L.376, R.382, A.402, V.403, D.404, G.405, G.436, C.440, E.463, D.464, D.465, S.597, D.598, T.599 Ligands: MN.18 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.376, C:A.402 Hydrogen bonds: C:I.374, C:G.405, C:E.463, C:S.597, C:S.597 Salt bridges: C:R.382 UDP.20: 17 residues within 4Å: Chain D: I.374, L.376, A.402, V.403, D.404, G.405, G.436, G.439, C.440, E.463, D.464, D.465, Y.595, S.597, D.598, T.599 Ligands: MN.22 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:L.376, D:A.402 Hydrogen bonds: D:G.405, D:E.463, D:D.464, D:Y.595, D:Y.595, D:S.597, D:D.598

6 x MN: MANGANESE (II) ION

MN.8: 4 residues within 4Å: Chain A: D.112, H.253, N.255 Ligands: UDP.7 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.253 MN.14: 4 residues within 4Å: Chain B: D.112, D.115, H.253 Ligands: UDP.13 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.112, 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: 2 residues within 4Å: Chain D: D.196 Ligands: GDU.19 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.196 MN.22: 2 residues within 4Å: Chain D: 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: 17 residues within 4Å: Chain C: L.87, A.88, R.89, D.119, W.163, R.167, H.170, V.171, R.175, D.194, D.196, H.263, S.264, D.293, I.294, P.322 Ligands: MN.17 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:R.89 Hydrogen bonds: C:L.87, C:R.89, C:R.89, C:R.167, C:R.175, C:H.263, C:S.264 Salt bridges: C:K.161 GDU.19: 20 residues within 4Å: Chain D: L.87, A.88, R.89, D.119, Y.154, W.163, R.167, H.170, V.171, R.175, D.194, A.195, D.196, H.263, 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: ABEF
Procollagen galactosyltransferase 1: CDGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
C

F
D

C
U

D
V

G
W

H
X

Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3

Procollagen galactosyltransferase 1

Related Entries With Identical Sequence