SMTL ID : 6te3.1

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

Coordinates

PDB Format Compare

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(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.10: 3 residues within 4Å: Chain B: H.523, E.524, N.525 No protein-ligand interaction detected (PLIP)

6 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, R.417, S.418, E.419 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.419 GOL.4: 10 residues within 4Å: Chain A: Y.241, N.244, G.407, S.418, D.420, L.424, W.433, N.434, V.435, P.436 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.244, A:S.418, A:D.420, A:N.434 GOL.11: 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.12: 5 residues within 4Å: Chain B: Q.238, Y.241, R.417, S.418, E.419 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.419 GOL.13: 10 residues within 4Å: Chain B: Y.241, N.244, G.407, S.418, D.420, L.424, W.433, N.434, V.435, P.436 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.244, B:S.418, B:D.420, B:N.434

2 x AKG: 2-OXOGLUTARIC ACID(Covalent)

AKG.5: 14 residues within 4Å: Chain A: R.576, Y.633, L.641, H.644, N.653, G.667, C.668, H.696, G.698, R.706, I.708, V.710, F.712 Ligands: FE2.6 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.633, A:Y.633, A:N.653, A:H.696 Salt bridges: A:R.576, A:H.644, A:H.696, A:R.706 AKG.14: 14 residues within 4Å: Chain B: R.576, Y.633, L.641, H.644, N.653, G.667, C.668, H.696, G.698, R.706, I.708, V.710, F.712 Ligands: FE2.15 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.633, B:N.653, B:H.696 Salt bridges: B:R.576, B:H.644, B:H.696, B:R.706

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

FE2.6: 5 residues within 4Å: Chain A: H.644, D.646, H.696, F.712 Ligands: AKG.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.644, A:D.646, A:D.646, A:H.696 FE2.7: 4 residues within 4Å: Chain A: H.572, D.574, D.588, H.590 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.572, A:D.574, A:D.574, A:D.588, A:D.588 FE2.15: 5 residues within 4Å: Chain B: H.644, D.646, H.696, F.712 Ligands: AKG.14 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.644, B:D.646, B:D.646, B:H.696 FE2.16: 4 residues within 4Å: Chain B: H.572, D.574, D.588, H.590 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.572, B:D.574, B:D.574, B:D.588, B:D.588

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

MN.8: 3 residues within 4Å: Chain A: D.89, D.92, H.230 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.89, A:D.92, A:D.92, A:H.230, H2O.6 MN.17: 3 residues within 4Å: Chain B: D.89, D.92, H.230 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.89, B:D.92, B:D.92, B:H.230, H2O.11

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

NAG.9: 2 residues within 4Å: Chain A: F.38, N.40 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.40 NAG.18: 2 residues within 4Å: Chain B: F.38, N.40 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.40

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

Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3

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