SMTL ID : 8rtp.2 (1 other biounit)

Bilirubin oxidase from Myrothecium verrucaria in complex with NAD+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

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: 8 residues within 4Å: Chain A: L.375, V.452, N.472, T.474, V.475, A.483, T.484, V.487 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.483 Water bridges: A:L.476 NAG-NAG.2: 6 residues within 4Å: Chain A: V.31, Y.481, N.482, E.525, Y.526, R.527 No protein-ligand interaction detected (PLIP)

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 SIN: SUCCINIC ACID(Non-covalent)

SIN.7: 10 residues within 4Å: Chain A: V.31, N.32, E.78, Y.121, R.125, R.527, P.528, Y.529, A.530, D.533 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.78, A:R.125, A:Y.529 Water bridges: A:N.29 Salt bridges: A:R.125

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 No protein-ligand interaction detected (PLIP)

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.9: 6 residues within 4Å: Chain A: S.299, G.304, T.305, N.394, N.416, R.436 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.299, A:N.394, A:N.416, A:R.436, A:R.436 Water bridges: A:D.308

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 4 residues within 4Å: Chain A: L.163, P.333, N.335, L.336 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.336 Water bridges: A:N.335, A:N.335

1 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.11: 9 residues within 4Å: Chain A: N.197, R.356, W.361, A.392, G.393, N.394, G.395, W.396, R.437 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.197, A:N.197, A:N.394, A:G.395 Water bridges: A:N.394, A:R.437, A:R.437 Salt bridges: A:R.437 pi-Stacking: A:W.396

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
BBB

Bilirubin oxidase

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