SMTL ID : 6tec.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 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.12: 4 residues within 4Å: Chain B: H.523, E.524, N.525, R.528 No protein-ligand interaction detected (PLIP)

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

UDX.2: 21 residues within 4Å: Chain A: V.21, A.22, T.23, W.52, V.57, T.60, V.61, G.62, G.63, K.66, D.89, S.90, Y.91, D.92, W.122, D.167, H.230, N.232, G.233, K.236 Ligands: MN.6 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.91 Hydrogen bonds: A:T.23, A:T.23, A:T.23, A:T.60, A:S.90, A:S.90, A:Y.91, A:D.92, A:D.167, A:G.233, A:G.233 Salt bridges: A:K.66, A:H.230, A:K.236, A:K.236 pi-Stacking: A:W.52, A:W.52 UDX.13: 21 residues within 4Å: Chain B: V.21, A.22, T.23, W.52, V.57, T.60, V.61, G.62, G.63, K.66, D.89, S.90, Y.91, D.92, W.122, D.167, H.230, N.232, G.233, K.236 Ligands: MN.17 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:Y.91 Hydrogen bonds: B:T.23, B:T.23, B:T.60, B:S.90, B:S.90, B:Y.91, B:Y.91, B:D.92, B:G.233, B:G.233 Salt bridges: B:K.66, B:H.230, B:K.236, B:K.236 pi-Stacking: B:W.52, B:W.52

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

AKG.3: 14 residues within 4Å: Chain A: R.576, Y.633, L.641, H.644, D.646, N.653, C.668, H.696, G.698, R.706, I.708, V.710, F.712 Ligands: FE2.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.641 Hydrogen bonds: A:Y.633, A:Y.633, A:D.646, A:N.653 Salt bridges: A:R.576, A:H.644, A:R.706 AKG.14: 14 residues within 4Å: Chain B: R.576, Y.633, L.641, H.644, D.646, N.653, 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 Hydrogen bonds: B:Y.633, B:D.646, B:N.653 Salt bridges: B:R.576, B:H.644, B:R.706

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

FE2.4: 4 residues within 4Å: Chain A: H.644, D.646, H.696 Ligands: AKG.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.644, A:D.646, A:D.646, A:H.696 FE2.5: 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:H.590 FE2.15: 4 residues within 4Å: Chain B: H.644, D.646, H.696 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:H.590

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

MN.6: 4 residues within 4Å: Chain A: D.89, D.92, H.230 Ligands: UDX.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.89, A:D.92, A:D.92, A:H.230 MN.17: 4 residues within 4Å: Chain B: D.89, D.92, H.230 Ligands: UDX.13 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.7: 2 residues within 4Å: Chain A: F.38, N.40 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.40 Water bridges: A:F.38, A:N.40 NAG.18: 2 residues within 4Å: Chain B: F.38, N.40 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.40 Water bridges: B:F.38, B:N.40

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 3 residues within 4Å: Chain A: E.25, K.389, E.452 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.389 Water bridges: A:E.452, A:E.452 EDO.9: 5 residues within 4Å: Chain A: E.27, L.30, N.387, K.389, R.445 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.387, A:R.445, A:R.445 Water bridges: A:T.26, A:E.27, A:K.389 EDO.10: 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:Y.241, A:E.419 EDO.11: 8 residues within 4Å: Chain A: Y.241, N.244, G.407, S.418, D.420, L.424, N.434, V.435 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.244, A:G.407 Water bridges: A:Y.241 EDO.19: 3 residues within 4Å: Chain B: E.25, K.389, E.452 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.389 Water bridges: B:E.452 EDO.20: 5 residues within 4Å: Chain B: E.27, L.30, N.387, K.389, R.445 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.387, B:R.445, B:R.445 Water bridges: B:T.26, B:K.389 EDO.21: 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:Y.241, B:E.419 EDO.22: 8 residues within 4Å: Chain B: Y.241, N.244, G.407, S.418, D.420, L.424, N.434, V.435 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.244, B:G.407 Water bridges: B:Y.241

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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