SMTL ID : 1jue.1

1.8 A resolution structure of native lactococcus lactis dihydroorotate dehydrogenase A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: K.33, A.34, S.35, A.37 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:K.33, A:S.35, H2O.1, H2O.2, H2O.5, H2O.5 MG.6: 3 residues within 4Å: Chain B: K.33, S.35, A.37 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:K.33, B:S.35, H2O.14, H2O.15, H2O.20

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 24 residues within 4Å: Chain A: A.18, S.19, G.20, V.21, K.43, S.44, Y.58, N.67, M.69, L.71, N.127, K.164, V.192, N.193, S.194, G.220, G.221, I.224, T.248, G.249, G.250, G.271, T.272 Ligands: ACY.3 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:V.21, A:Y.58, A:Y.58 Hydrogen bonds: A:S.19, A:S.44, A:S.44, A:S.44, A:N.127, A:K.164, A:K.164, A:N.193, A:G.221, A:G.250, A:G.271, A:T.272 Water bridges: A:S.19, A:S.19, A:N.67, A:S.99, A:G.249, A:I.251, A:I.251, A:I.251 FMN.7: 24 residues within 4Å: Chain B: A.18, S.19, G.20, V.21, K.43, S.44, Y.58, N.67, M.69, L.71, N.127, K.164, V.192, N.193, S.194, G.220, G.221, I.224, T.248, G.249, G.250, G.271, T.272 Ligands: ACY.8 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:V.21, B:Y.58, B:Y.58 Hydrogen bonds: B:S.19, B:S.44, B:S.44, B:S.44, B:N.127, B:K.164, B:K.164, B:N.193, B:G.221, B:G.250, B:G.271, B:T.272, B:T.272 Water bridges: B:S.19, B:S.19, B:N.67, B:E.125, B:G.249, B:I.251, B:I.251, B:A.273

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.3: 9 residues within 4Å: Chain A: K.43, N.67, M.69, G.70, L.71, P.72, C.130, N.132 Ligands: FMN.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.70, A:L.71, A:N.132 Salt bridges: A:K.43 ACY.8: 9 residues within 4Å: Chain B: K.43, N.67, M.69, G.70, L.71, P.72, C.130, N.132 Ligands: FMN.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.70, B:L.71, B:N.132 Salt bridges: B:K.43

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: Y.168, F.169, H.173 Chain B: Y.141, F.169, H.173 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:F.169, A:H.173, B:F.169, B:H.173 GOL.5: 5 residues within 4Å: Chain A: N.8, A.9, K.10, E.93, G.94 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.10, A:G.94 GOL.9: 7 residues within 4Å: Chain A: K.213, D.214, F.216 Chain B: L.171, A.234, T.237, R.238 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:K.213, A:D.214, A:D.214, B:T.237, B:R.238, B:R.238 GOL.10: 7 residues within 4Å: Chain A: L.171, A.234, T.237, R.238 Chain B: K.213, D.214, F.216 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.237, A:R.238, A:R.238, B:K.213 GOL.11: 4 residues within 4Å: Chain B: A.9, K.10, E.93, G.94 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.10, B:K.10, B:G.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Norager, S. et al., Lactococcus lactis dihydroorotate dehydrogenase A mutants reveal important facets of the enzymatic function. J.Biol.Chem. (2003)

Release Date

2003-09-09

Peptides

dihydroorotate dehydrogenase A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

dihydroorotate dehydrogenase A

Related Entries With Identical Sequence