SMTL ID : 1qpa.1

LIGNIN PEROXIDASE ISOZYME LIP4.65 (PI 4.65)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG-FUC.1: 6 residues within 4Å: Chain B: E.251, S.254, N.257, N.258, K.261 Ligands: MAN.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.251, B:S.254, B:K.261 Water bridges: B:N.258

1 x MAN- MAN: alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose(Post Translational Modification)

MAN-MAN.2: 4 residues within 4Å: Chain B: T.308, H.309, A.310, T.323 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.308, B:T.308, B:H.309, B:A.310

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

NAG.3: 4 residues within 4Å: Chain A: N.257, N.258, K.261, E.264 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.258, A:E.264

5 x MAN: alpha-D-mannopyranose(Post Translational Modification)

MAN.4: 4 residues within 4Å: Chain A: S.333, V.334, A.335 Chain B: P.295 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.334 Water bridges: A:S.333, A:R.336, A:R.336 MAN.5: 6 residues within 4Å: Chain A: P.229, L.230, K.231, K.307, S.331, A.332 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.231, A:K.307, A:K.307 MAN.9: 4 residues within 4Å: Chain A: P.295 Chain B: S.333, V.334, A.335 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Water bridges: A:A.292, A:P.293, A:P.293, B:R.336, B:R.336 MAN.10: 6 residues within 4Å: Chain B: P.229, L.230, K.231, K.307, S.331, A.332 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.231, B:K.307, B:K.307 Water bridges: B:T.214 MAN.11: 4 residues within 4Å: Chain B: C.316, S.318, T.319 Ligands: NAG-NAG-FUC.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.318, B:S.318 Water bridges: B:Q.253

4 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: S.178, D.195, T.197, Q.200, D.202 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.195, A:D.195, A:T.197, A:Q.200, A:D.202 CA.7: 4 residues within 4Å: Chain A: D.49, G.67, D.69, S.71 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.49, A:D.69, A:S.71, H2O.5, H2O.5 CA.12: 5 residues within 4Å: Chain B: S.178, D.195, T.197, Q.200, D.202 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.195, B:D.195, B:T.197, B:Q.200, B:D.202 CA.13: 4 residues within 4Å: Chain B: D.49, G.67, D.69, S.71 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.49, B:D.69, B:S.71, H2O.11, H2O.11

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.8: 23 residues within 4Å: Chain A: H.40, E.41, L.43, R.44, F.47, I.86, P.146, E.147, P.148, L.173, L.174, A.176, H.177, I.179, A.180, A.181, A.182, N.183, D.184, V.185, F.194, L.236, T.238 22 PLIP interactions: 21 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:L.43, A:F.47, A:F.47, A:F.47, A:F.47, A:L.173, A:L.174, A:A.176, A:A.180, A:F.194, A:F.194 Hydrogen bonds: A:H.40, A:I.86, A:A.181, A:N.183, A:N.183, A:D.184, A:V.185 Water bridges: A:R.44 Salt bridges: A:R.44 Metal complexes: A:H.177, H2O.1 HEM.14: 24 residues within 4Å: Chain B: H.40, E.41, L.43, R.44, F.47, I.86, P.146, E.147, P.148, L.173, L.174, A.176, H.177, I.179, A.180, A.181, A.182, N.183, D.184, V.185, F.194, L.236, T.238, L.273 26 PLIP interactions: 25 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:L.43, B:R.44, B:F.47, B:F.47, B:F.47, B:F.47, B:F.47, B:P.146, B:P.146, B:P.148, B:L.173, B:A.176, B:A.180, B:F.194, B:L.273 Hydrogen bonds: B:H.40, B:I.86, B:A.181, B:N.183, B:N.183, B:D.184, B:V.185 Salt bridges: B:R.44 pi-Stacking: B:F.194 Metal complexes: B:H.177, H2O.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Choinowski, T. et al., The crystal structure of lignin peroxidase at 1.70 A resolution reveals a hydroxy group on the cbeta of tryptophan 171: a novel radical site formed during the redox cycle. J.Mol.Biol. (1999)

Release Date

1997-01-11

Peptides

LIGNIN PEROXIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

LIGNIN PEROXIDASE