SMTL ID : 2rab.1

Structure of glutathione amide reductase from Chromatium gracile in complex with NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 37 residues within 4Å: Chain A: I.10, G.11, G.13, S.14, G.15, I.33, E.34, S.35, K.36, A.37, G.40, T.41, C.42, V.45, G.46, C.47, K.50, G.112, H.113, A.114, A.137, T.138, G.139, I.177, R.262, L.269, G.301, D.302, Q.308, L.309, T.310, P.311, A.313, F.343 Chain B: H.437, P.438 Ligands: NAD.2 27 PLIP interactions: 25 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.177 Hydrogen bonds: A:G.12, A:S.14, A:S.14, A:G.15, A:S.35, A:T.41, A:T.41, A:C.42, A:K.50, A:A.114, A:A.114, A:D.302, A:Q.308, A:T.310, A:T.310, B:H.437 Water bridges: A:G.13, A:G.16, A:S.35, A:A.37, A:G.40, A:T.41, A:G.139, A:G.140, A:A.313, B:H.437 FAD.9: 38 residues within 4Å: Chain A: H.437, P.438 Chain B: I.10, G.11, G.12, G.13, S.14, G.15, I.33, E.34, S.35, K.36, A.37, G.40, T.41, C.42, V.45, G.46, C.47, K.50, G.112, H.113, A.114, A.137, T.138, G.139, F.160, R.262, L.269, G.301, D.302, Q.308, L.309, T.310, P.311, A.313, F.343 Ligands: NAD.10 30 PLIP interactions: 28 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.160 Hydrogen bonds: B:G.12, B:S.14, B:S.14, B:G.15, B:S.35, B:T.41, B:T.41, B:T.41, B:C.42, B:K.50, B:A.114, B:A.114, B:D.302, B:Q.308, B:T.310, B:T.310, B:T.310, A:H.437 Water bridges: B:G.13, B:S.35, B:A.37, B:G.40, B:G.139, B:G.140, B:G.140, B:G.140, B:I.303, B:A.313, A:H.437

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 24 residues within 4Å: Chain A: K.50, I.172, G.173, A.174, G.175, Y.176, I.177, E.180, A.196, L.197, E.198, F.228, A.229, V.230, A.259, V.260, G.261, R.262, Q.308, L.309, T.340, V.341, F.343 Ligands: FAD.1 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.176, A:Y.176, A:I.177 Hydrogen bonds: A:A.174, A:G.175, A:I.177, A:E.180, A:L.197, A:E.198, A:V.230, A:V.230, A:A.259, A:G.261, A:Q.308, A:T.340 Water bridges: A:G.178, A:L.202, A:V.260 NAD.10: 23 residues within 4Å: Chain B: K.50, I.172, G.173, A.174, G.175, Y.176, I.177, E.180, A.196, L.197, E.198, F.228, A.229, V.230, A.259, V.260, G.261, Q.308, L.309, T.340, V.341, F.343 Ligands: FAD.9 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.176, B:Y.176, B:I.177 Hydrogen bonds: B:A.174, B:G.175, B:I.177, B:E.180, B:L.197, B:E.198, B:V.230, B:V.230, B:A.259, B:G.261 Water bridges: B:G.178, B:F.203, B:V.260

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

CL.3: 1 residues within 4Å: Chain A: R.104 Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain A: R.115 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: H.113, R.267 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: H.345 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain B: R.104 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain B: R.115 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: N.265, T.266, R.267 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain B: H.58, H.345 Ligand excluded by PLIP

4 x NI: NICKEL (II) ION(Non-covalent)

NI.5: 2 residues within 4Å: Chain A: D.118, H.120 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.120, H2O.9, H2O.10, H2O.10, H2O.10 NI.7: 4 residues within 4Å: Chain A: T.2, Q.3, H.4, F.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.4 NI.13: 2 residues within 4Å: Chain B: D.118, H.120 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.120, H2O.18, H2O.18, H2O.19 NI.15: 4 residues within 4Å: Chain B: T.2, Q.3, H.4, F.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Van Petegem, F. et al., Understanding nicotinamide dinucleotide cofactor and substrate specificity in class I flavoprotein disulfide oxidoreductases: crystallographic analysis of a glutathione amide reductase. J.Mol.Biol. (2007)

Release Date

2008-02-19

Peptides

glutathione amide reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

glutathione amide reductase

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