SMTL ID : 2yg4.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 36 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 Ligands: 4HA.9 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:R.43, A:W.385, A:A.394, A:Y.395 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:Q.65, A:D.434 Salt bridges: A:R.43, A:R.43 pi-Stacking: A:Y.395, A:H.432 FAD.8: 34 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, P.234, V.235, A.263, V.264, I.272, W.385, W.390, A.394, Y.395, C.422, S.423, Q.431, H.432, V.433, A.436 Ligands: 4HA.2 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:R.43, B:W.385, B:A.394 Hydrogen bonds: 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:W.390, B:S.423, B:S.423, B:Q.431, B:V.433 Water bridges: B:G.14, B:G.17, B:G.42, B:D.434 Salt bridges: B:R.43, B:R.43 pi-Stacking: B:Y.395, B:H.432

2 x 4HA: 4-HYDROXYBUTAN-1-AMINIUM(Non-covalent)

4HA.2: 6 residues within 4Å: Chain B: G.172, M.173, E.324, Y.395, H.432 Ligands: FAD.8 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.395 Hydrogen bonds: B:E.324 Water bridges: B:Y.395 4HA.9: 8 residues within 4Å: Chain A: G.172, M.173, L.206, E.324, F.341, Y.395, H.432 Ligands: FAD.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.206 Hydrogen bonds: A:E.324

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 11 residues within 4Å: Chain A: A.131, E.132, W.135, L.188, F.399, S.411, R.412, I.425, A.426, A.427, Y.430 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.131, A:S.411, A:S.411, A:R.412, A:R.412 Water bridges: A:Q.289, A:Y.430 GOL.4: 8 residues within 4Å: Chain A: R.412, P.414, H.419, F.420, M.439, R.442, T.443, D.446 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.419, A:F.420, A:F.420, A:R.442 GOL.7: 8 residues within 4Å: Chain A: T.46, V.53, L.54, E.55, R.209, G.212, G.213, N.330 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.53, A:R.209, A:G.212 Water bridges: A:G.212, A:N.330, A:H.331 GOL.10: 7 residues within 4Å: Chain B: R.412, P.414, H.419, F.420, M.439, T.443, D.446 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.420, B:D.446

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

SO4.5: 2 residues within 4Å: Chain A: R.141 Chain B: K.149 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Water bridges: B:K.149, B:K.149, A:R.141 Salt bridges: B:K.149, A:R.141 SO4.6: 4 residues within 4Å: Chain A: L.353, S.354, A.355, R.358 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.353, A:A.355 Water bridges: A:R.358, A:R.358 Salt bridges: A:R.358 SO4.11: 4 residues within 4Å: Chain A: D.348, F.351 Chain B: R.280, R.281 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.281 Salt bridges: B:R.280, B:R.281 SO4.12: 4 residues within 4Å: Chain B: L.353, S.354, A.355, R.358 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Water bridges: A:R.280, B:L.353, B:R.358 Hydrogen bonds: B:A.355 Salt bridges: B:R.358

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

Related Entries With Identical Sequence