SMTL ID : 2yg5.1

Structure-based redesign of cofactor binding in Putrescine Oxidase: A394C mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 37 residues within 4Å: Chain A: V.11, G.12, A.13, 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, C.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 Hydrogen bonds: A:G.14, 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:W.390, A:S.423, A:S.423, A:Q.431, A:V.433 Water bridges: A:G.17, A:G.42, A:Q.65, A:D.434 Salt bridges: A:R.43, A:R.43 pi-Stacking: A:W.390, A:Y.395 FAD.8: 37 residues within 4Å: Chain B: V.11, G.12, A.13, 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, C.394, Y.395, C.422, S.423, Q.431, H.432, V.433, A.436 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:R.43, B:W.385 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:W.390, 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:W.390, B:Y.395

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

SO4.2: 9 residues within 4Å: Chain A: D.157, D.158, A.159, E.160 Chain B: D.157, D.158, A.159, E.160 Ligands: SO4.9 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.158, A:A.159, A:E.160, B:A.159, B:E.160 Water bridges: A:T.111, A:T.111, A:D.158, B:T.111 SO4.3: 3 residues within 4Å: Chain A: R.162 Chain B: N.108, E.160 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.108 Water bridges: B:S.92, B:N.108, B:E.160, A:R.162 Salt bridges: A:R.162 SO4.6: 3 residues within 4Å: Chain A: F.80, E.81, H.331 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.81 SO4.9: 9 residues within 4Å: Chain A: D.157, D.158, A.159, E.160 Chain B: D.157, D.158, A.159, E.160 Ligands: SO4.2 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:A.159, A:E.160, B:D.158, B:A.159, B:E.160 Water bridges: A:T.111, A:E.160 SO4.10: 3 residues within 4Å: Chain A: N.108, E.160 Chain B: R.162 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.108 Water bridges: A:S.92, A:N.108, A:E.160, B:R.162 Salt bridges: B:R.162 SO4.13: 3 residues within 4Å: Chain B: F.80, E.81, H.331 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.81

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: W.135, L.188, F.399, L.404, S.411, R.412, I.425, A.426, Y.430 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.411, A:S.411, A:R.412, A:A.426 Water bridges: A:F.399, A:Y.430 GOL.5: 5 residues within 4Å: Chain A: I.153, N.154, Q.155, S.156, D.157 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.155 Water bridges: A:D.157, A:D.157 GOL.7: 3 residues within 4Å: Chain A: S.354, A.355, R.358 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.355, A:R.358 Water bridges: A:L.353, A:S.354, A:E.356 GOL.11: 9 residues within 4Å: Chain B: W.135, L.188, F.399, L.404, S.411, R.412, I.425, A.426, Y.430 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.411, B:S.411, B:R.412, B:A.426, B:Y.430 Water bridges: B:F.399, B:Y.430 GOL.12: 5 residues within 4Å: Chain B: I.153, N.154, Q.155, S.156, D.157 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.155 Water bridges: B:D.157, B:D.157, A:T.110 GOL.14: 3 residues within 4Å: Chain B: S.354, A.355, R.358 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.355, B:R.358 Water bridges: B:L.353, B:S.354, B:E.356

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
A

PUTRESCINE OXIDASE