SMTL ID : 3q6j.1

Structural basis for carbon dioxide binding by 2-ketopropyl coenzyme M Oxidoreductase/Carboxylase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-dimer

Ligands

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

NAP.1: 19 residues within 4Å: Chain A: H.90, L.189, G.222, S.223, K.224, T.225, E.228, R.245, T.246, K.250, G.311, L.312, G.313, K.332, M.359, E.360, F.390, L.391 Ligands: FAD.2 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:K.224, A:K.224 Hydrogen bonds: A:G.222, A:K.224, A:R.245, A:T.246, A:E.314, A:M.359, A:E.360, A:E.360 Water bridges: A:T.188, A:S.223, A:S.223, A:K.224, A:E.247, A:K.250, A:K.250, A:N.277, A:G.313, A:K.332, A:D.389 Salt bridges: A:R.245, A:K.250, A:K.332 pi-Cation interactions: A:R.245, A:R.245 NAP.9: 19 residues within 4Å: Chain B: H.90, L.189, G.222, S.223, K.224, T.225, E.228, R.245, T.246, K.250, G.311, L.312, G.313, E.314, K.332, M.359, E.360, F.390 Ligands: FAD.10 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:K.224, B:K.224 Hydrogen bonds: B:G.222, B:G.222, B:K.224, B:T.246, B:E.314, B:M.359, B:E.360 Water bridges: B:T.188, B:S.223, B:K.224, B:R.245, B:R.245, B:R.245, B:R.245, B:R.245, B:T.246, B:T.246, B:K.250, B:G.313, B:G.313, B:G.313, B:E.360, B:E.360 Salt bridges: B:R.245, B:K.250, B:K.332 pi-Cation interactions: B:R.245, B:R.245

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

FAD.2: 30 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, C.156, P.157, A.158, A.181, V.182, G.183, H.202, Y.229, G.352, D.353, M.359, E.360, M.361, A.364 Chain B: F.501 Ligands: NAP.1 33 PLIP interactions: 32 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.86, A:H.90, A:H.202, A:Y.229 Hydrogen bonds: A:G.52, A:A.54, A:R.74, A:W.75, A:S.81, A:A.158, A:D.353, A:M.359, A:M.361, B:F.501 Water bridges: A:A.53, A:G.55, A:R.74, A:R.74, A:R.74, A:R.74, A:R.74, A:G.80, A:S.81, A:S.81, A:C.82, A:A.184, A:A.184, A:D.353, A:L.354, A:L.354, A:F.362 pi-Cation interactions: A:R.74, A:K.224 FAD.10: 31 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, F.390 Ligands: NAP.9 34 PLIP interactions: 33 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.86, B:H.202, B:Y.229 Hydrogen bonds: B:G.52, B:A.53, B:A.54, B:R.74, B:W.75, B:G.79, B:S.81, B:S.81, B:A.158, B:A.158, B:D.353, B:M.359, B:E.360, B:M.361, A:F.501 Water bridges: B:G.55, B:R.74, B:R.74, B:R.74, B:R.74, B:G.80, B:C.82, B:G.183, B:A.184, B:R.317, B:D.353, B:L.354, B:E.360, B:F.362 pi-Cation interactions: B:R.74, B:K.224

1 x KPC: (2-[2-KETOPROPYLTHIO]ETHANESULFONATE(Non-covalent)

KPC.3: 15 residues within 4Å: Chain A: A.53, R.56, F.57, G.79, C.82, P.83, V.88, P.136, M.140, M.361, R.365 Chain B: L.431, F.501 Ligands: BCT.5, CO2.6 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.136, B:L.431 Salt bridges: A:R.56, A:R.365

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: L.427, V.429, L.431, A.447, S.450 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:V.429, A:L.431, A:A.447, A:S.450, H2O.7 MG.12: 5 residues within 4Å: Chain B: L.427, V.429, L.431, A.447, S.450 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:V.429, B:L.431, B:A.447, B:S.450, H2O.24

2 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.5: 6 residues within 4Å: Chain A: R.365 Chain B: L.431, F.501, H.506, Q.509 Ligands: KPC.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.506 BCT.8: 6 residues within 4Å: Chain A: L.431, F.501, H.506, Q.509 Chain B: R.365 Ligands: ACN.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.506

1 x CO2: CARBON DIOXIDE(Non-covalent)

CO2.6: 7 residues within 4Å: Chain A: V.88, P.136 Chain B: A.430, L.431, A.433, F.442 Ligands: KPC.3 No protein-ligand interaction detected (PLIP)

1 x ACN: ACETONE(Non-covalent)

ACN.7: 5 residues within 4Å: Chain A: L.431, F.501 Chain B: M.140 Ligands: BCT.8, COM.11 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.431, A:F.501

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

COM.11: 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.7 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.56, B:R.365

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pandey, A.S. et al., Structural basis for carbon dioxide binding by 2-ketopropyl coenzyme M oxidoreductase/carboxylase. Febs Lett. (2011)

Release Date

2011-02-16

Peptides

2-oxopropyl-CoM reductase, carboxylating: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

2-oxopropyl-CoM reductase, carboxylating

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