SMTL ID : 6teu.1

Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Val80Lys mutant - Cocrystal with Fe2+, Mn2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 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(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: H.523, E.524, N.525 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: H.523, E.524, N.525 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: A.24, E.25, T.26, K.389, E.452 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.389 GOL.3: 5 residues within 4Å: Chain A: Q.238, Y.241, A.408, S.418, E.419 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.419 GOL.10: 5 residues within 4Å: Chain B: A.24, E.25, T.26, K.389, E.452 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.389 GOL.11: 5 residues within 4Å: Chain B: Q.238, Y.241, A.408, S.418, E.419 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.419

2 x AKG: 2-OXOGLUTARIC ACID(Covalent)

AKG.4: 11 residues within 4Å: Chain A: R.576, Y.633, L.641, H.644, N.653, C.668, H.696, G.698, R.706, I.708 Ligands: FE2.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.633, A:Y.633, A:N.653 Salt bridges: A:R.576, A:H.644, A:H.696, A:R.706 AKG.12: 11 residues within 4Å: Chain B: R.576, Y.633, L.641, H.644, N.653, C.668, H.696, G.698, R.706, I.708 Ligands: FE2.13 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.633, B:N.653 Salt bridges: B:R.576, B:H.644, B:H.696, B:R.706

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

FE2.5: 5 residues within 4Å: Chain A: H.644, D.646, H.696, F.712 Ligands: AKG.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.644, A:D.646, A:D.646, A:H.696 FE2.6: 4 residues within 4Å: Chain A: H.572, D.574, D.588, H.590 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.572, A:D.574, A:D.588, A:D.588 FE2.13: 5 residues within 4Å: Chain B: H.644, D.646, H.696, F.712 Ligands: AKG.12 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.644, B:D.646, B:D.646, B:H.696 FE2.14: 4 residues within 4Å: Chain B: H.572, D.574, D.588, H.590 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.572, B:D.574, B:D.588, B:D.588

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

MN.7: 3 residues within 4Å: Chain A: D.89, D.92, H.230 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.89, A:D.92, A:D.92 MN.15: 3 residues within 4Å: Chain B: D.89, D.92, H.230 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.89, B:D.92, B:D.92

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

NAG.8: 2 residues within 4Å: Chain A: F.38, N.40 No protein-ligand interaction detected (PLIP) NAG.16: 2 residues within 4Å: Chain B: F.38, N.40 No protein-ligand interaction detected (PLIP)

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

2021-05-19

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

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