SMTL ID : 2c3c.1

2.01 Angstrom X-ray crystal structure of a mixed disulfide between coenzyme M and NADPH-dependent oxidoreductase 2-ketopropyl coenzyme M carboxylase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

2 x COM: 1-THIOETHANESULFONIC ACID(Non-covalent)

COM.1: 12 residues within 4Å: Chain A: A.53, R.56, F.57, G.79, C.82, P.83, V.88, M.140, M.361, R.365 Chain B: F.501 Ligands: ACN.7 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.56, A:R.365 COM.5: 12 residues within 4Å: Chain A: F.501 Chain B: A.53, R.56, F.57, G.79, C.82, P.83, V.88, M.140, M.361, R.365 Ligands: ACN.3 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.56, B:R.365

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.2: 31 residues within 4Å: Chain A: G.50, G.52, A.53, A.54, V.72, D.73, R.74, W.75, G.80, S.81, A.86, C.87, H.90, H.91, P.157, A.158, A.181, V.182, G.183, H.202, Y.229, E.314, G.352, D.353, M.359, E.360, M.361, A.364, F.390 Chain B: F.501 Ligands: NAP.4 25 PLIP interactions: 24 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.86, A:H.202, A:Y.229 Hydrogen bonds: A:A.54, A:R.74, A:S.81, A:A.158, A:D.353, A:M.359, A:M.361, B:F.501 Water bridges: A:G.52, A:G.55, A:R.74, A:R.74, A:G.80, A:S.81, A:A.158, A:A.184, A:A.184, A:R.317, A:D.353, A:L.354, A:L.354, A:F.362 FAD.6: 30 residues within 4Å: Chain A: F.501 Chain B: G.50, G.52, A.53, A.54, V.72, D.73, R.74, W.75, G.80, S.81, A.86, C.87, H.90, H.91, P.157, A.158, A.181, V.182, G.183, H.202, Y.229, E.314, G.352, D.353, M.359, E.360, M.361, A.364 Ligands: NAP.8 27 PLIP interactions: 26 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.86, B:H.202, B:Y.229 Hydrogen bonds: B:A.54, B:R.74, B:S.81, B:S.81, B:A.158, B:A.158, B:R.317, B:D.353, B:M.359, B:E.360, B:M.361, A:F.501 Water bridges: B:G.52, B:G.55, B:R.74, B:R.74, B:G.80, B:G.183, B:A.184, B:A.184, B:L.354, B:E.360, B:F.362 pi-Cation interactions: B:R.74

2 x ACN: ACETONE(Non-covalent)

ACN.3: 7 residues within 4Å: Chain A: L.431, F.501, H.506, Q.509 Chain B: M.140, R.365 Ligands: COM.5 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.431, A:F.501, A:F.501 Hydrogen bonds: A:Q.509, B:R.365, B:R.365 Water bridges: B:R.56 ACN.7: 6 residues within 4Å: Chain A: R.365 Chain B: L.431, F.501, H.506, Q.509 Ligands: COM.1 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.431, B:F.501 Hydrogen bonds: B:Q.509, A:R.365 Water bridges: A:R.56

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.4: 19 residues within 4Å: Chain A: H.90, L.189, G.221, G.222, S.223, K.224, T.225, E.228, V.244, R.245, T.246, K.250, G.311, L.312, G.313, M.359, E.360, F.390 Ligands: FAD.2 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:K.224, A:K.224 Hydrogen bonds: A:G.222, A:S.223, A:K.224, A:T.225, A:R.245, A:T.246, A:E.247, A:G.311, A:M.359, A:E.360 Water bridges: A:K.224, A:T.225, A:T.225, A:A.226, A:R.245, A:R.245, A:E.247, A:K.250, A:K.250, A:N.277, A:G.313, A:E.360, A:E.360 Salt bridges: A:R.245, A:K.250 pi-Cation interactions: A:R.245, A:R.245 NAP.8: 19 residues within 4Å: Chain B: H.90, L.189, G.221, G.222, S.223, K.224, T.225, E.228, R.245, T.246, K.250, G.311, L.312, G.313, E.314, M.359, E.360, F.390 Ligands: FAD.6 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:K.224, B:K.224 Hydrogen bonds: B:G.222, B:S.223, B:K.224, B:T.225, B:T.225, B:R.245, B:R.245, B:T.246, B:G.311, B:G.313, B:M.359, B:E.360 Water bridges: B:T.188, B:T.188, B:A.226, B:R.245, B:T.246, B:E.247, B:N.277, B:E.360 Salt bridges: B:R.245, B:K.250 pi-Cation interactions: B:R.245, B:R.245

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pandey, A.S. et al., Mechanistic Implications of the Structure of the Mixed-Disulfide Intermediate of the Disulfide Oxidoreductase, 2-Ketopropyl-Coenzyme M Oxidoreductase/Carboxylase. Biochemistry (2006)

Release Date

2005-12-12

Peptides

2-OXOPROPYL-COM REDUCTASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

2-OXOPROPYL-COM REDUCTASE

Related Entries With Identical Sequence