SMTL ID : 5zw2.1

FAD complex of PigA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 30 residues within 4Å: Chain A: N.125, A.126, A.127, T.128, G.133, S.134, F.158, I.159, T.160, W.211, P.360, I.363, F.364, T.367, D.369, I.370 Chain B: R.270, Q.272, F.273, I.277, F.280, V.283, R.286, Q.338, T.339, G.341, G.342 Chain D: Q.281 Ligands: EDO.4, ACT.12 28 PLIP interactions: 17 interactions with chain A, 10 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: A:I.363, A:F.364 Hydrogen bonds: A:N.125, A:A.127, A:T.128, A:T.128, A:S.134, A:S.134, A:T.160, A:T.367, A:D.369, B:Q.272, B:R.286, B:Q.338, B:G.342, D:Q.281 Water bridges: A:T.128, A:G.133, A:S.365, A:T.367, A:N.368, B:Y.266, B:R.270, B:A.343 pi-Stacking: A:W.211, B:F.280 Salt bridges: B:R.270, B:R.270 FAD.14: 30 residues within 4Å: Chain A: R.270, Q.272, F.273, I.277, F.280, V.283, R.286, Q.338, T.339, G.341, G.342 Chain B: N.125, A.126, A.127, T.128, G.133, S.134, F.158, I.159, T.160, W.211, P.360, I.363, F.364, T.367, D.369, I.370 Chain C: Q.281 Ligands: EDO.17, ACT.25 28 PLIP interactions: 10 interactions with chain A, 17 interactions with chain B, 1 interactions with chain C Hydrogen bonds: A:Q.272, A:R.286, A:Q.338, A:G.342, B:N.125, B:A.127, B:T.128, B:T.128, B:S.134, B:S.134, B:T.160, B:T.367, B:D.369, C:Q.281 Water bridges: A:Y.266, A:R.270, A:A.343, B:T.128, B:G.133, B:S.365, B:T.367, B:N.368 Salt bridges: A:R.270, A:R.270 pi-Stacking: A:F.280, B:W.211 Hydrophobic interactions: B:I.363, B:F.364 FAD.27: 30 residues within 4Å: Chain B: Q.281 Chain C: N.125, A.126, A.127, T.128, G.133, S.134, F.158, I.159, T.160, W.211, P.360, I.363, F.364, T.367, D.369, I.370 Chain D: R.270, Q.272, F.273, I.277, F.280, V.283, R.286, Q.338, T.339, G.341, G.342 Ligands: EDO.30, ACT.38 29 PLIP interactions: 11 interactions with chain D, 17 interactions with chain C, 1 interactions with chain B Hydrogen bonds: D:Q.272, D:R.286, D:Q.338, D:G.342, C:N.125, C:A.127, C:T.128, C:T.128, C:S.134, C:S.134, C:T.160, C:T.160, C:T.367, C:T.367, B:Q.281 Water bridges: D:R.270, D:Q.338, D:A.343, D:A.343, C:T.128, C:G.133, C:S.365, C:T.367 Salt bridges: D:R.270, D:R.270 pi-Stacking: D:F.280, C:W.211 Hydrophobic interactions: C:I.363, C:F.364 FAD.40: 30 residues within 4Å: Chain A: Q.281 Chain C: R.270, Q.272, F.273, I.277, F.280, V.283, R.286, Q.338, T.339, G.341, G.342 Chain D: N.125, A.126, A.127, T.128, G.133, S.134, F.158, I.159, T.160, W.211, P.360, I.363, F.364, T.367, D.369, I.370 Ligands: EDO.43, ACT.51 29 PLIP interactions: 11 interactions with chain C, 17 interactions with chain D, 1 interactions with chain A Hydrogen bonds: C:Q.272, C:R.286, C:Q.338, C:G.342, D:N.125, D:A.127, D:T.128, D:T.128, D:S.134, D:S.134, D:T.160, D:T.160, D:T.367, D:T.367, A:Q.281 Water bridges: C:R.270, C:Q.338, C:A.343, C:A.343, D:T.128, D:G.133, D:S.365, D:T.367 Salt bridges: C:R.270, C:R.270 pi-Stacking: C:F.280, D:W.211 Hydrophobic interactions: D:I.363, D:F.364

8 x O4B: 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE(Non-covalent)

O4B.2: 3 residues within 4Å: Chain A: E.40, L.41, K.44 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.44 O4B.3: 6 residues within 4Å: Chain A: F.273, K.275, Q.279, F.280 Ligands: EDO.17, O4B.29 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.275 O4B.15: 3 residues within 4Å: Chain B: E.40, L.41, K.44 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.44 O4B.16: 6 residues within 4Å: Chain B: F.273, K.275, Q.279, F.280 Ligands: EDO.4, O4B.42 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.275 O4B.28: 3 residues within 4Å: Chain C: E.40, L.41, K.44 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.40, C:K.44 O4B.29: 6 residues within 4Å: Chain C: F.273, K.275, Q.279, F.280 Ligands: O4B.3, EDO.43 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.275 O4B.41: 3 residues within 4Å: Chain D: E.40, L.41, K.44 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.40, D:K.44 O4B.42: 6 residues within 4Å: Chain D: F.273, K.275, Q.279, F.280 Ligands: O4B.16, EDO.30 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.275

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

EDO.4: 4 residues within 4Å: Chain A: E.373 Chain B: F.280 Ligands: FAD.1, O4B.16 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: L.5, Y.13, L.71, E.74, R.298, Y.302 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: Y.13, Y.17, K.78 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: I.157, F.158, I.201, W.211, S.212, E.213 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: D.289, L.292, R.293, Q.296, Y.328 Chain D: L.324, Y.328 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: L.260, L.264, K.291 Chain D: L.379 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: R.258, L.259, T.262 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: F.280 Chain B: E.373 Ligands: O4B.3, FAD.14 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain B: L.5, Y.13, L.71, E.74, R.298, Y.302 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain B: Y.13, Y.17, K.78 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain B: I.157, F.158, I.201, W.211, S.212, E.213 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain B: D.289, L.292, R.293, Q.296, Y.328 Chain C: L.324, Y.328 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain B: L.260, L.264, K.291 Chain C: L.379 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain B: R.258, L.259, T.262 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain C: E.373 Chain D: F.280 Ligands: FAD.27, O4B.42 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain C: L.5, Y.13, L.71, E.74, R.298, Y.302 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain C: Y.13, Y.17, K.78 Ligand excluded by PLIP EDO.33: 6 residues within 4Å: Chain C: I.157, F.158, I.201, W.211, S.212, E.213 Ligand excluded by PLIP EDO.34: 7 residues within 4Å: Chain B: L.324, Y.328 Chain C: D.289, L.292, R.293, Q.296, Y.328 Ligand excluded by PLIP EDO.35: 4 residues within 4Å: Chain B: L.379 Chain C: L.260, L.264, K.291 Ligand excluded by PLIP EDO.36: 3 residues within 4Å: Chain C: R.258, L.259, T.262 Ligand excluded by PLIP EDO.43: 4 residues within 4Å: Chain C: F.280 Chain D: E.373 Ligands: O4B.29, FAD.40 Ligand excluded by PLIP EDO.44: 6 residues within 4Å: Chain D: L.5, Y.13, L.71, E.74, R.298, Y.302 Ligand excluded by PLIP EDO.45: 3 residues within 4Å: Chain D: Y.13, Y.17, K.78 Ligand excluded by PLIP EDO.46: 6 residues within 4Å: Chain D: I.157, F.158, I.201, W.211, S.212, E.213 Ligand excluded by PLIP EDO.47: 7 residues within 4Å: Chain A: L.324, Y.328 Chain D: D.289, L.292, R.293, Q.296, Y.328 Ligand excluded by PLIP EDO.48: 4 residues within 4Å: Chain A: L.379 Chain D: L.260, L.264, K.291 Ligand excluded by PLIP EDO.49: 3 residues within 4Å: Chain D: R.258, L.259, T.262 Ligand excluded by PLIP

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

ACT.11: 3 residues within 4Å: Chain A: R.31, I.36, S.38 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.36 Hydrogen bonds: A:S.38 Water bridges: A:D.27, A:R.31, A:Q.34 ACT.12: 5 residues within 4Å: Chain A: G.133, S.134, F.237, G.366 Ligands: FAD.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.237 Water bridges: A:G.133 ACT.24: 3 residues within 4Å: Chain B: R.31, I.36, S.38 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.36 Hydrogen bonds: B:S.38 Water bridges: B:D.27, B:R.31, B:Q.34 ACT.25: 5 residues within 4Å: Chain B: G.133, S.134, F.237, G.366 Ligands: FAD.14 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.237 Water bridges: B:G.133 ACT.37: 3 residues within 4Å: Chain C: R.31, I.36, S.38 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.36 Hydrogen bonds: C:S.38 Water bridges: C:R.31, C:Q.34 ACT.38: 5 residues within 4Å: Chain C: G.133, S.134, F.237, G.366 Ligands: FAD.27 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.237 Water bridges: C:G.133 ACT.50: 3 residues within 4Å: Chain D: R.31, I.36, S.38 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.36 Hydrogen bonds: D:S.38 Water bridges: D:R.31, D:Q.34 ACT.51: 5 residues within 4Å: Chain D: G.133, S.134, F.237, G.366 Ligands: FAD.40 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.237 Water bridges: D:G.133

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

CL.13: 3 residues within 4Å: Chain A: Q.281 Chain C: Q.281 Ligands: CL.39 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain B: Q.281 Chain D: Q.281 Ligands: CL.52 Ligand excluded by PLIP CL.39: 3 residues within 4Å: Chain A: Q.281 Chain C: Q.281 Ligands: CL.13 Ligand excluded by PLIP CL.52: 3 residues within 4Å: Chain B: Q.281 Chain D: Q.281 Ligands: CL.26 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, C.-C. et al., Crystal Structure of PigA: A Prolyl Thioester-Oxidizing Enzyme in Prodigiosin Biosynthesis. Chembiochem (2019)

Release Date

2018-09-05

Peptides

L-prolyl-[peptidyl-carrier protein] dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

L-prolyl-[peptidyl-carrier protein] dehydrogenase

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