SMTL ID : 9ey7.1

Crystal structure of human tyrosinase-related protein 1 (TYRP1) in complex with (R)-2,4-dihydroxyphenylalanine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-FUC.1: 8 residues within 4Å: Chain A: L.12, R.13, S.14, G.15, L.68, R.69, F.70, N.72 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.69, A:R.69 Water bridges: A:R.13, A:R.13

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 7 residues within 4Å: Chain A: R.140, E.156, S.268, D.271, Y.272, L.275, N.280 No protein-ligand interaction detected (PLIP)

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.3: 4 residues within 4Å: Chain A: P.53, Y.55, Y.324, N.326 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain A: G.293, N.294, V.295, A.296, N.361, G.362 No protein-ligand interaction detected (PLIP)

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.5: 2 residues within 4Å: Chain A: R.4, N.157 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.157

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: D.388, E.389, R.392, P.433, T.439, Y.440, W.444 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.388, A:T.439, A:Y.440, A:W.444 GOL.7: 6 residues within 4Å: Chain A: N.118, V.121, R.122, D.239, S.257, V.258 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.118, A:R.122, A:S.257, A:V.258 GOL.8: 6 residues within 4Å: Chain A: K.128, R.129, Q.261, W.262, R.263, E.283 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.263, A:R.263 Water bridges: A:D.125, A:V.258

4 x ZN: ZINC ION(Non-covalent)

ZN.9: 6 residues within 4Å: Chain A: H.168, H.191, H.200, F.376 Ligands: ZN.10, OTY.13 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.168, A:H.191, A:H.200, H2O.1 ZN.10: 5 residues within 4Å: Chain A: H.353, H.357, H.380 Ligands: ZN.9, OTY.13 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.353, A:H.357, A:H.380, H2O.1 ZN.11: 2 residues within 4Å: Chain A: E.42, H.76 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.42, A:H.76, H2O.1, H2O.2 ZN.12: 3 residues within 4Å: Chain A: H.51, H.57, E.64 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.51, A:H.57, A:E.64, A:E.64

1 x OTY: 2-hydroxy-L-tyrosine(Non-covalent)

OTY.13: 13 residues within 4Å: Chain A: H.168, H.191, Y.338, R.350, H.353, N.354, H.357, L.358, G.365, T.367, S.370 Ligands: ZN.9, ZN.10 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:N.354 Hydrogen bonds: A:T.367, A:S.370, A:S.370 Water bridges: A:T.367 Salt bridges: A:R.350 pi-Stacking: A:H.357

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Faure, C. et al., Interactions of Phenylalanine Derivatives with Human Tyrosinase: Lessons from Experimental and Theoretical tudies. Chembiochem (2024)

Release Date

2024-05-22

Peptides

5,6-dihydroxyindole-2-carboxylic acid oxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

5,6-dihydroxyindole-2-carboxylic acid oxidase

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