SMTL ID : 6i3j.2 (1 other biounit)

Bilirubin oxidase from Myrothecium verrucaria in complex with ferricyanide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 8 residues within 4Å: Chain A: L.375, V.452, N.472, T.474, V.475, A.483, T.484, V.487 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.483, A:T.484 Water bridges: A:V.475

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: 7 residues within 4Å: Chain A: V.31, N.482, E.525, Y.526, R.527 Ligands: FC6.11, NA.14 1 PLIP interactions: 1 interactions with chain A Water bridges: 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: 5 residues within 4Å: Chain A: H.136, H.401, H.403, M.454, H.456 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.136, A:H.403, A:H.456 CU.5: 5 residues within 4Å: Chain A: H.94, H.96, W.132, H.134, H.458 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.96, A:H.134, A:H.458 CU.6: 4 residues within 4Å: Chain A: H.94, H.96, H.401, H.403 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.94, A:H.401

5 x FC6: HEXACYANOFERRATE(3-)(Non-covalent)

FC6.7: 4 residues within 4Å: Chain A: G.393, N.394, G.395, W.396 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.394, A:G.395 Water bridges: A:R.437, A:R.437 FC6.8: 3 residues within 4Å: Chain A: T.184, A.185, N.186 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.185, A:N.186, A:N.186 FC6.9: 3 residues within 4Å: Chain A: P.14, K.214, N.215 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.215, A:N.215 FC6.10: 5 residues within 4Å: Chain A: P.344, R.386, K.408, I.410, E.443 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.386, A:R.386, A:K.408 FC6.11: 4 residues within 4Å: Chain A: G.480, Y.481, N.482 Ligands: NAG-NAG.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.481, A:N.482 Water bridges: A:G.480

2 x SIN: SUCCINIC ACID(Non-covalent)

SIN.12: 9 residues within 4Å: Chain A: N.32, E.78, Y.121, R.125, R.527, P.528, Y.529, A.530, D.533 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.32, A:Y.529, A:D.533 Salt bridges: A:R.125 SIN.13: 10 residues within 4Å: Chain A: S.66, A.145, Y.146, G.148, Q.149, A.150, T.179, K.181, H.205, G.208 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.179 Hydrogen bonds: A:S.66 Water bridges: A:G.208 Salt bridges: A:K.181, A:K.181

3 x NA: SODIUM ION(Non-functional Binders)

NA.14: 4 residues within 4Å: Chain A: T.522, E.525, Y.526 Ligands: NAG-NAG.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.522, A:E.525 NA.15: 2 residues within 4Å: Chain A: S.284, D.285 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.284 NA.16: 2 residues within 4Å: Chain A: E.261, D.338 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.261, A:D.338

1 x PGR: R-1,2-PROPANEDIOL(Non-covalent)

PGR.17: 5 residues within 4Å: Chain A: E.195, S.198, F.199, W.200, Y.309 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.200, A:G.201, A:Y.309

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koval, T. et al., Trp-His covalent adduct in bilirubin oxidase is crucial for effective bilirubin binding but has a minor role in electron transfer. Sci Rep (2019)

Release Date

2019-10-02

Peptides

Bilirubin oxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Bilirubin oxidase

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