SMTL ID : 2yg3.1

Structure-based redesign of cofactor binding in Putrescine Oxidase: wild type enzyme

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 35 residues within 4Å: Chain A: V.11, G.12, G.14, P.15, S.16, I.34, E.35, A.36, R.37, G.41, G.42, R.43, T.44, I.56, G.57, G.58, Q.59, W.60, P.234, V.235, A.263, V.264, P.265, L.268, I.272, W.385, W.390, A.394, Y.395, C.422, S.423, Q.431, H.432, V.433, A.436 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:R.43, A:W.385, A:A.394 Hydrogen bonds: A:S.16, A:A.36, A:R.37, A:G.41, A:R.43, A:G.58, A:Q.59, A:W.60, A:W.60, A:V.235, A:V.235, A:S.423, A:S.423, A:Q.431, A:V.433 Water bridges: A:G.14, A:G.17, A:G.42, A:D.434 Salt bridges: A:R.43, A:R.43 pi-Stacking: A:Y.395, A:Y.395, A:H.432 FAD.7: 36 residues within 4Å: Chain B: V.11, G.12, G.14, P.15, S.16, I.34, E.35, A.36, R.37, G.41, G.42, R.43, T.44, I.56, G.57, G.58, Q.59, W.60, A.233, P.234, V.235, A.263, V.264, P.265, L.268, I.272, W.385, W.390, A.394, Y.395, C.422, S.423, Q.431, H.432, V.433, A.436 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:R.43, B:W.385, B:A.394 Hydrogen bonds: B:G.14, B:S.16, B:A.36, B:R.37, B:G.41, B:R.43, B:G.58, B:Q.59, B:W.60, B:W.60, B:V.235, B:V.235, B:S.423, B:S.423, B:Q.431, B:V.433 Water bridges: B:G.17, B:G.42, B:Q.65, B:D.434 Salt bridges: B:R.43, B:R.43 pi-Stacking: B:Y.395, B:Y.395, B:H.432

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: K.239, W.240, N.241, G.244, A.245, T.246 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.241, A:G.244 Water bridges: A:W.240, A:W.240, A:A.245 GOL.4: 5 residues within 4Å: Chain A: L.353, S.354, A.355, R.358 Chain B: R.280 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:A.355, B:R.280, B:R.280 Water bridges: A:L.353, A:S.354, A:E.356 GOL.6: 9 residues within 4Å: Chain A: R.412, P.414, H.419, F.420, M.439, R.442, T.443, D.446 Ligands: SO4.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.420, A:F.420, A:R.442, A:D.446, A:D.446 GOL.8: 4 residues within 4Å: Chain A: R.280 Chain B: S.354, A.355, R.358 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:R.280, B:A.355, B:R.358 Water bridges: B:L.353, B:S.354, B:E.356, B:R.358 GOL.9: 8 residues within 4Å: Chain B: R.412, P.414, H.419, F.420, M.439, R.442, T.443, D.446 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.420, B:F.420, B:R.442, B:D.446

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: R.412, R.442 Ligands: GOL.6 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.412, A:R.412 Salt bridges: A:R.442 SO4.5: 5 residues within 4Å: Chain A: K.149, P.177, A.178, H.179 Chain B: R.141 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.178, A:H.179, B:R.141 Salt bridges: A:K.149, A:H.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kopacz, M.M. et al., Structure-Based Redesign of Cofactor Binding in Putrescine Oxidase. Biochemistry (2011)

Release Date

2011-05-18

Peptides

PUTRESCINE OXIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PUTRESCINE OXIDASE

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