SMTL ID : 6fxm.1

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

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.11: 4 residues within 4Å: Chain B: H.523, E.524, N.525, R.528 No protein-ligand interaction detected (PLIP)

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: A.24, E.25, T.26, K.389, E.452 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.389, A:E.452 GOL.3: 5 residues within 4Å: Chain A: L.237, Q.238, Y.241, S.418, E.419 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.237, A:E.419 Water bridges: A:Y.241 GOL.4: 5 residues within 4Å: Chain A: R.44, T.45, L.46, G.47, W.69 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.45, A:G.47, A:W.69 GOL.5: 9 residues within 4Å: Chain A: Y.241, N.244, G.407, S.418, D.420, L.424, W.433, N.434, V.435 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.244, A:G.407, A:S.418, A:N.434 GOL.12: 5 residues within 4Å: Chain B: A.24, E.25, T.26, K.389, E.452 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.389, B:E.452 GOL.13: 5 residues within 4Å: Chain B: L.237, Q.238, Y.241, S.418, E.419 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.237, B:E.419 Water bridges: B:Y.241 GOL.14: 5 residues within 4Å: Chain B: R.44, T.45, L.46, G.47, W.69 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.45, B:G.47, B:W.69 GOL.15: 9 residues within 4Å: Chain B: Y.241, N.244, G.407, S.418, D.420, L.424, W.433, N.434, V.435 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.244, B:G.407, B:S.418, B:N.434

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

AKG.6: 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: FE2.7 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.16: 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: FE2.17 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 FE2: FE (II) ION(Non-covalent)

FE2.7: 4 residues within 4Å: Chain A: H.644, D.646, H.696 Ligands: AKG.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.644, A:D.646, A:D.646, A:H.696 FE2.17: 4 residues within 4Å: Chain B: H.644, D.646, H.696 Ligands: AKG.16 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.644, B:D.646, B:D.646, B:H.696

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

MN.8: 3 residues within 4Å: Chain A: D.89, D.92, H.230 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.89, A:D.92, A:H.230, H2O.6, H2O.10 MN.9: 3 residues within 4Å: Chain A: D.574, D.588, H.590 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.574, A:D.574, A:D.588, A:D.588, H2O.5 MN.18: 3 residues within 4Å: Chain B: D.89, D.92, H.230 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.89, B:D.92, B:H.230, H2O.16, H2O.20 MN.19: 3 residues within 4Å: Chain B: D.574, D.588, H.590 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.574, B:D.574, B:D.588, B:D.588, H2O.15

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

NAG.10: 2 residues within 4Å: Chain A: F.38, N.40 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.40 NAG.20: 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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