SMTL ID : 6fxr.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 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.10: 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: 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.419 Water bridges: A:L.237 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, A.408, S.418, E.419 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.419 Water bridges: B:L.237

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

AKG.4: 15 residues within 4Å: Chain A: R.576, Y.633, L.641, H.644, D.646, 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 Hydrophobic interactions: A:L.641, A:I.708 Hydrogen bonds: A:Y.633, A:Y.633, A:N.653 Salt bridges: A:R.576, A:H.644, A:R.706 AKG.13: 15 residues within 4Å: Chain B: R.576, Y.633, L.641, H.644, D.646, 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 Hydrophobic interactions: B:L.641, B:I.708 Hydrogen bonds: B:Y.633, B:N.653 Salt bridges: B:R.576, B:H.644, B:R.706

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

UDP.5: 15 residues within 4Å: Chain A: V.21, A.22, T.23, W.52, V.57, K.66, D.89, S.90, Y.91, D.92, H.230, N.232, G.233, K.236 Ligands: MN.8 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.91 Hydrogen bonds: A:V.21, A:T.23, A:T.23, A:T.23, A:S.90, A:Y.91, A:G.233 Salt bridges: A:H.230, A:K.236, A:K.236 pi-Stacking: A:W.52 UDP.14: 15 residues within 4Å: Chain B: V.21, A.22, T.23, W.52, V.57, K.66, D.89, S.90, Y.91, D.92, H.230, N.232, G.233, K.236 Ligands: MN.17 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.91 Hydrogen bonds: B:V.21, B:T.23, B:T.23, B:S.90, B:Y.91, B:Y.91, B:G.233 Salt bridges: B:H.230, B:K.236, B:K.236 pi-Stacking: B:W.52

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

FE2.6: 4 residues within 4Å: Chain A: H.644, D.646, H.696 Ligands: AKG.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.644, 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.588, A:D.588, A:H.590 FE2.15: 4 residues within 4Å: Chain B: H.644, D.646, H.696 Ligands: AKG.13 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.644, 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.588, B:D.588, B:H.590

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

MN.8: 5 residues within 4Å: Chain A: D.89, D.92, H.230, K.236 Ligands: UDP.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.89, A:D.92, A:D.92, A:H.230 MN.17: 5 residues within 4Å: Chain B: D.89, D.92, H.230, K.236 Ligands: UDP.14 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.89, B:D.92, B:D.92, B:H.230

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

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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