SMTL ID : 8rto.1 (3 other biounits)

Bilirubin oxidase from Myrothecium verrucaria in complex with ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

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.1: 7 residues within 4Å: Chain A: L.375, V.452, N.472, T.474, V.475, T.484, V.487 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.476

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 4 residues within 4Å: Chain A: N.482, E.525, Y.526, R.527 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.525, A:E.525, A:R.527

4 x CU: COPPER (II) ION(Non-covalent)

CU.3: 6 residues within 4Å: Chain A: T.397, H.398, C.457, N.459, H.462, M.467 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.398, A:C.457, A:H.462 CU.4: 6 residues within 4Å: Chain A: H.136, H.401, H.403, H.456 Ligands: CU.6, OXY.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.136, A:H.403, A:H.456 CU.5: 6 residues within 4Å: Chain A: H.94, H.96, W.132, H.134, H.458 Ligands: OXY.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.96, A:H.134, A:H.458 CU.6: 6 residues within 4Å: Chain A: H.94, H.96, H.401, H.403 Ligands: CU.4, OXY.8 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.94, A:H.401

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.7: 8 residues within 4Å: Chain A: N.197, R.356, W.361, G.393, N.394, G.395, W.396, R.437 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.197, A:N.197, A:A.392, A:N.394, A:G.395 Water bridges: A:R.356, A:R.437, A:R.437 Salt bridges: A:R.437, A:R.437 pi-Stacking: A:W.396

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.8: 11 residues within 4Å: Chain A: H.94, H.96, H.134, H.136, H.401, H.403, H.456, H.458 Ligands: CU.4, CU.5, CU.6 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.134, A:E.463

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 2 residues within 4Å: Chain A: R.350, Q.351 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain A: R.527 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Svecova, L. et al., Bilirubin oxidase - answers to questions on ligand binding and Trp-His covalent link formation. To be published

Release Date

2025-08-06

Peptides

Bilirubin oxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

Bilirubin oxidase

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