SMTL ID : 6fxk.1

Crystal Structure of full-length Human Lysyl Hydroxylase LH3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 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: 4 residues within 4Å: Chain A: H.523, E.524, N.525, R.528 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: H.523, E.524, N.525, R.528 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: E.25, T.26, K.389, E.452 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.389 GOL.3: 3 residues within 4Å: Chain A: Y.241, S.418, E.419 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.417, A:E.419 GOL.8: 4 residues within 4Å: Chain B: E.25, T.26, K.389, E.452 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.389 GOL.9: 3 residues within 4Å: Chain B: Y.241, S.418, E.419 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.417, B:E.419

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

AKG.4: 12 residues within 4Å: Chain A: Y.633, L.641, H.644, D.646, G.667, C.668, H.696, G.698, R.706, I.708, F.712 Ligands: FE2.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.641 Hydrogen bonds: A:Y.633, A:Y.633 Salt bridges: A:H.644, A:H.696, A:R.706 AKG.10: 12 residues within 4Å: Chain B: Y.633, L.641, H.644, D.646, G.667, C.668, H.696, G.698, R.706, I.708, F.712 Ligands: FE2.11 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.641 Hydrogen bonds: B:Y.633 Salt bridges: B:H.644, B:H.696, B:R.706

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

FE2.5: 4 residues within 4Å: Chain A: H.644, D.646, H.696 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 FE2.11: 4 residues within 4Å: Chain B: H.644, D.646, H.696 Ligands: AKG.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.644, B:D.646, B:D.646, B:H.696

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

NAG.6: 3 residues within 4Å: Chain A: F.38, F.39, N.40 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.39 Hydrogen bonds: A:F.38, A:N.40 NAG.12: 3 residues within 4Å: Chain B: F.38, F.39, N.40 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.39 Hydrogen bonds: B:F.38, B:N.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Scietti, L. et al., Molecular architecture of the multifunctional collagen lysyl hydroxylase and glycosyltransferase LH3. Nat Commun (2018)

Release Date

2018-08-22

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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