SMTL ID : 3ntd.1

Structure of the Shewanella loihica PV-4 NADH-dependent persulfide reductase C531S Mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-dimer

Ligands

2 x COA: COENZYME A(Non-covalent)

COA.1: 30 residues within 4Å: Chain A: V.10, A.11, A.14, A.18, R.19, R.22, S.39, F.40, N.42, C.43, L.61, Q.62, F.67, F.71, A.321, N.325, R.329 Chain B: V.380, Y.388, Y.446, K.454, Q.459, F.462, V.463, N.466, V.533, G.534, L.535, N.538 Ligands: FAD.3 25 PLIP interactions: 13 interactions with chain B, 12 interactions with chain A Hydrogen bonds: B:K.454, B:K.454, B:Q.459, B:N.466, B:N.466, B:V.533, A:F.40, A:N.325, A:N.325 Water bridges: B:H.381, B:N.538, B:N.538, B:N.538, B:N.538, A:R.22, A:R.22 Salt bridges: B:K.454, B:K.454, A:R.19, A:R.22, A:R.22, A:R.329 Hydrophobic interactions: A:V.10, A:Q.62, A:F.67 COA.6: 29 residues within 4Å: Chain A: Y.446, K.454, Q.459, F.462, V.463, N.466, V.533, G.534, L.535, N.538 Chain B: V.10, A.11, A.14, S.15, A.18, R.19, R.22, S.39, F.40, N.42, C.43, L.61, Q.62, F.67, F.71, A.321, N.325, R.329 Ligands: FAD.5 23 PLIP interactions: 8 interactions with chain A, 15 interactions with chain B Hydrogen bonds: A:Q.459, A:N.466, A:N.466, A:V.533, A:N.538, B:S.15, B:F.40, B:N.325 Water bridges: A:H.381, A:K.454, B:R.19, B:R.19, B:R.22, B:R.22, B:N.325 Salt bridges: A:K.454, B:R.19, B:R.22, B:R.22, B:R.329 Hydrophobic interactions: B:V.10, B:Q.62, B:F.67

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 6 residues within 4Å: Chain A: S.531, Q.532, V.533, G.534, L.535, R.536 Ligand excluded by PLIP CL.4: 6 residues within 4Å: Chain B: S.531, Q.532, V.533, G.534, L.535, R.536 Ligand excluded by PLIP

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

FAD.3: 32 residues within 4Å: Chain A: I.7, G.8, V.10, A.11, G.12, F.32, E.33, R.34, N.42, C.43, P.46, H.79, E.80, V.81, S.112, P.113, G.114, L.133, R.134, F.161, I.162, L.271, G.302, D.303, P.319, L.320, A.321, A.324 Chain B: Y.446, A.447, P.448 Ligands: COA.1 30 PLIP interactions: 29 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.46, A:L.133, A:I.162 Hydrogen bonds: A:A.11, A:G.12, A:R.34, A:R.34, A:N.42, A:N.42, A:N.42, A:V.81, A:V.81, A:D.303, A:P.319, A:A.321, B:Y.446 Water bridges: A:V.10, A:G.13, A:R.34, A:G.114, A:A.115, A:R.134, A:R.134, A:R.134, A:R.134, A:G.322, A:A.324 Salt bridges: A:R.134 pi-Stacking: A:F.161 pi-Cation interactions: A:R.34 FAD.5: 31 residues within 4Å: Chain A: Y.446, A.447, P.448 Chain B: I.7, G.8, V.10, A.11, G.12, F.32, E.33, R.34, N.42, C.43, H.79, E.80, V.81, S.112, P.113, G.114, L.133, R.134, F.161, I.162, L.271, G.302, D.303, P.319, L.320, A.321, A.324 Ligands: COA.6 34 PLIP interactions: 33 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.133, B:F.161, B:I.162, B:I.162 Hydrogen bonds: B:A.11, B:G.12, B:R.34, B:R.34, B:N.42, B:N.42, B:N.42, B:E.80, B:V.81, B:V.81, B:G.114, B:D.303, B:P.319, B:A.321, A:Y.446 Water bridges: B:V.10, B:G.13, B:A.115, B:A.115, B:R.134, B:R.134, B:R.134, B:R.134, B:N.135, B:A.304, B:G.322, B:A.324 Salt bridges: B:R.134 pi-Stacking: B:F.161 pi-Cation interactions: B:R.34

Links

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Citation

Warner, M.D. et al., Characterization of an NADH-Dependent Persulfide Reductase from Shewanella loihica PV-4: Implications for the Mechanism of Sulfur Respiration via FAD-Dependent Enzymes . Biochemistry (2010)

Release Date

2010-12-08

Peptides

FAD-dependent pyridine nucleotide-disulphide oxidoreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

FAD-dependent pyridine nucleotide-disulphide oxidoreductase