SMTL ID : 8one.1

Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Asp190Ser mutant - Cocrystal with Fe2+, Mn2+, UDP-Glucose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG.1: 4 residues within 4Å: Chain A: H.524, E.525, N.526, R.529 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: H.524, E.525, N.526, R.529 No protein-ligand interaction detected (PLIP)

2 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.2: 15 residues within 4Å: Chain A: R.577, F.630, Y.634, L.642, H.645, D.647, N.654, C.669, H.697, G.699, R.707, I.709, V.711, F.713 Ligands: FE2.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.642, A:I.709 Hydrogen bonds: A:Y.634, A:Y.634, A:D.647, A:N.654 Salt bridges: A:R.577, A:H.645, A:R.707 AKG.12: 15 residues within 4Å: Chain B: R.577, F.630, Y.634, L.642, H.645, D.647, N.654, C.669, H.697, G.699, R.707, I.709, V.711, F.713 Ligands: FE2.13 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.642, B:I.709 Hydrogen bonds: B:Y.634, B:D.647, B:N.654 Salt bridges: B:R.577, B:H.645, B:R.707

4 x FE2: FE (II) ION(Non-covalent)

FE2.3: 4 residues within 4Å: Chain A: H.645, D.647, H.697 Ligands: AKG.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.645, A:D.647, A:D.647, A:H.697 FE2.4: 4 residues within 4Å: Chain A: H.573, D.575, D.589, H.591 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.573, A:D.575, A:D.589, A:D.589, A:H.591 FE2.13: 4 residues within 4Å: Chain B: H.645, D.647, H.697 Ligands: AKG.12 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.645, B:D.647, B:D.647, B:H.697 FE2.14: 4 residues within 4Å: Chain B: H.573, D.575, D.589, H.591 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.573, B:D.575, B:D.589, B:D.589, B:H.591

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

MN.5: 4 residues within 4Å: Chain A: D.90, D.93, H.231 Ligands: UPG.10 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.90, A:D.93, A:D.93, A:H.231 MN.15: 4 residues within 4Å: Chain B: D.90, D.93, H.231 Ligands: UPG.20 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.90, B:D.93, B:D.93, B:H.231

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.6: 2 residues within 4Å: Chain A: F.39, N.41 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.41 Water bridges: A:F.39 NAG.16: 2 residues within 4Å: Chain B: F.39, N.41 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.41 Water bridges: B:F.39

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: A.25, E.26, K.390, E.453 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.390 Water bridges: A:E.26 GOL.8: 4 residues within 4Å: Chain A: Q.239, Y.242, S.419, E.420 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.420 Water bridges: A:L.238 GOL.9: 9 residues within 4Å: Chain A: Y.242, N.245, G.408, S.419, D.421, L.425, W.434, N.435, V.436 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.245, A:G.408, A:S.419, A:N.435 Water bridges: A:Y.242 GOL.17: 4 residues within 4Å: Chain B: A.25, E.26, K.390, E.453 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.390 Water bridges: B:E.26 GOL.18: 4 residues within 4Å: Chain B: Q.239, Y.242, S.419, E.420 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.420 Water bridges: B:L.238 GOL.19: 9 residues within 4Å: Chain B: Y.242, N.245, G.408, S.419, D.421, L.425, W.434, N.435, V.436 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.245, B:G.408, B:S.419, B:N.435 Water bridges: B:Y.242

2 x UPG: URIDINE-5'-DIPHOSPHATE-GLUCOSE(Non-covalent)

UPG.10: 22 residues within 4Å: Chain A: V.22, A.23, T.24, W.53, V.58, T.61, G.63, G.64, K.67, D.90, S.91, Y.92, D.93, W.123, S.144, G.145, D.169, H.231, N.233, G.234, K.237 Ligands: MN.5 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.92 Hydrogen bonds: A:V.22, A:T.24, A:T.24, A:T.24, A:V.58, A:K.67, A:S.91, A:Y.92, A:S.144, A:G.234 Salt bridges: A:K.237, A:K.237 pi-Stacking: A:W.53, A:W.53 UPG.20: 22 residues within 4Å: Chain B: V.22, A.23, T.24, W.53, V.58, T.61, G.63, G.64, K.67, D.90, S.91, Y.92, D.93, W.123, S.144, G.145, D.169, H.231, N.233, G.234, K.237 Ligands: MN.15 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:Y.92 Hydrogen bonds: B:V.22, B:T.24, B:T.24, B:V.58, B:K.67, B:S.91, B:Y.92, B:Y.92, B:D.93, B:D.93, B:S.144, B:G.234 Water bridges: B:T.24, B:T.24 Salt bridges: B:K.237, B:K.237 pi-Stacking: B:W.53, B:W.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mattoteia, D. et al., Identification of Regulatory Molecular "Hot Spots" for LH/PLOD Collagen Glycosyltransferase Activity. Int J Mol Sci (2023)

Release Date

2023-07-19

Peptides

Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3