SMTL ID : 3vqr.1

Structure of a dye-linked L-proline dehydrogenase mutant from the aerobic hyperthermophilic archaeon, Aeropyrum pernix

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 37 residues within 4Å: Chain A: V.29, G.30, G.32, V.33, V.34, V.53, D.54, A.55, S.61, G.62, D.63, S.64, R.66, S.67, M.68, A.69, A.70, R.202, R.203, V.204, A.249, A.250, G.251, W.253, R.272, V.274, Q.322, G.370, H.371, Y.372, T.396, G.398, S.399, G.400, I.401, M.402 Ligands: ACT.2 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:R.272, A:V.274, A:Y.372 Hydrogen bonds: A:G.32, A:V.34, A:A.55, A:G.56, A:S.61, A:G.62, A:D.63, A:S.64, A:M.68, A:A.70, A:A.70, A:V.204, A:V.204, A:T.396, A:G.400, A:I.401, A:M.402 Water bridges: A:A.31, A:G.35, A:G.60, A:S.61, A:G.251, A:T.396, A:G.398 pi-Stacking: A:Y.372 FAD.5: 38 residues within 4Å: Chain B: V.29, G.30, G.32, V.33, V.34, V.53, D.54, A.55, G.56, S.61, G.62, D.63, S.64, R.66, S.67, M.68, A.69, A.70, R.202, R.203, V.204, A.249, A.250, G.251, W.253, R.272, V.274, Q.322, G.370, H.371, Y.372, T.396, G.398, S.399, G.400, I.401, M.402 Ligands: ACT.6 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:R.272, B:V.274, B:Y.372 Hydrogen bonds: B:G.32, B:V.34, B:A.55, B:G.56, B:S.61, B:G.62, B:D.63, B:D.63, B:S.64, B:M.68, B:A.70, B:A.70, B:V.204, B:V.204, B:G.400, B:I.401, B:M.402 Water bridges: B:A.31, B:G.35, B:G.60, B:S.61, B:T.396, B:G.398 pi-Stacking: B:Y.372

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 8 residues within 4Å: Chain A: D.63, G.251, V.252, W.253, H.371, D.373, T.396 Ligands: FAD.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.373 Hydrogen bonds: A:V.252 ACT.6: 7 residues within 4Å: Chain B: D.63, G.251, V.252, H.371, D.373, T.396 Ligands: FAD.5 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:D.373 Hydrogen bonds: B:D.63, B:V.252, B:D.373 Water bridges: B:T.396, B:T.396

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 9 residues within 4Å: Chain A: G.251, V.252, S.254, N.255, T.265, S.267, R.268, P.269, D.373 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.251, A:T.265, A:R.268, A:D.373 EDO.4: 7 residues within 4Å: Chain A: I.263, D.264, F.266, F.383, W.386, L.436 Chain B: F.331 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.264, A:D.264 EDO.7: 8 residues within 4Å: Chain B: G.251, V.252, N.255, T.265, S.267, R.268, P.269, D.373 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.251, B:R.268 EDO.8: 6 residues within 4Å: Chain B: I.263, D.264, F.266, F.383, P.385, W.386 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.264, B:D.264

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sakuraba, H. et al., Crystal Structure of Novel Dye-linked L-Proline Dehydrogenase from Hyperthermophilic Archaeon Aeropyrum pernix. J.Biol.Chem. (2012)

Release Date

2012-04-25

Peptides

Putative oxidoreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative oxidoreductase