SMTL ID : 5zw7.1

FAD-PigA complex at 1.3 A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 28 residues within 4Å: Chain A: N.125, A.127, T.128, G.133, S.134, F.158, I.159, T.160, K.203, W.211, P.360, I.363, 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: GOL.7 33 PLIP interactions: 1 interactions with chain D, 21 interactions with chain A, 11 interactions with chain B Hydrogen bonds: D:Q.281, 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 Hydrophobic interactions: A:I.363 Water bridges: A:N.125, A:N.125, A:N.125, A:N.125, A:T.128, A:G.133, A:S.365, A:T.367, A:N.368, A:E.373, B:R.270, B:G.341, B:A.343, B:A.343 pi-Stacking: A:W.211, B:F.280 Salt bridges: B:R.270, B:R.270 FAD.9: 28 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.127, T.128, G.133, S.134, F.158, I.159, T.160, K.203, W.211, P.360, I.363, T.367, D.369, I.370 Chain C: Q.281 Ligands: GOL.15 33 PLIP interactions: 11 interactions with chain A, 21 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:R.270, A:G.341, A:A.343, A:A.343, B:N.125, B:N.125, B:N.125, B:N.125, B:T.128, B:G.133, B:S.365, B:T.367, B:N.368, B:E.373 Salt bridges: A:R.270, A:R.270 pi-Stacking: A:F.280, B:W.211 Hydrophobic interactions: B:I.363 FAD.17: 28 residues within 4Å: Chain B: Q.281 Chain C: N.125, A.127, T.128, G.133, S.134, F.158, I.159, T.160, K.203, W.211, P.360, I.363, 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: GOL.23 33 PLIP interactions: 21 interactions with chain C, 11 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: C:I.363 Hydrogen bonds: 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, D:Q.272, D:R.286, D:Q.338, D:G.342, B:Q.281 Water bridges: C:N.125, C:N.125, C:N.125, C:N.125, C:T.128, C:G.133, C:S.365, C:T.367, C:N.368, D:R.270, D:G.341, D:A.343, D:A.343 pi-Stacking: C:W.211, D:F.280 Salt bridges: D:R.270, D:R.270 FAD.25: 28 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.127, T.128, G.133, S.134, F.158, I.159, T.160, K.203, W.211, P.360, I.363, T.367, D.369, I.370 Ligands: GOL.31 33 PLIP interactions: 11 interactions with chain C, 21 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:G.341, C:A.343, C:A.343, D:N.125, D:N.125, D:N.125, D:N.125, D:T.128, D:G.133, D:S.365, D:T.367, D:N.368 Salt bridges: C:R.270, C:R.270 pi-Stacking: C:F.280, D:W.211 Hydrophobic interactions: D:I.363

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

O4B.2: 4 residues within 4Å: Chain A: V.23, E.40, L.41, K.44 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.44 O4B.10: 4 residues within 4Å: Chain B: V.23, E.40, L.41, K.44 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.44 O4B.18: 4 residues within 4Å: Chain C: V.23, E.40, L.41, K.44 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.40, C:K.44 O4B.26: 4 residues within 4Å: Chain D: V.23, E.40, L.41, K.44 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.40, D:K.44

20 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: L.5, Y.13, E.74, R.298, Y.302 Ligand excluded by PLIP GOL.4: 4 residues within 4Å: Chain A: Y.13, E.14, Y.17, K.78 Ligand excluded by PLIP GOL.5: 7 residues within 4Å: Chain A: R.81, R.258, L.259, T.262, G.350, L.351, H.354 Ligand excluded by PLIP GOL.6: 7 residues within 4Å: Chain A: R.303, K.307, A.316, D.317, M.320 Chain D: K.291, E.295 Ligand excluded by PLIP GOL.7: 7 residues within 4Å: Chain A: G.133, S.134, I.136, F.237, G.366, I.370 Ligands: FAD.1 Ligand excluded by PLIP GOL.11: 5 residues within 4Å: Chain B: L.5, Y.13, E.74, R.298, Y.302 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain B: Y.13, E.14, Y.17, K.78 Ligand excluded by PLIP GOL.13: 7 residues within 4Å: Chain B: R.81, R.258, L.259, T.262, G.350, L.351, H.354 Ligand excluded by PLIP GOL.14: 7 residues within 4Å: Chain B: R.303, K.307, A.316, D.317, M.320 Chain C: K.291, E.295 Ligand excluded by PLIP GOL.15: 7 residues within 4Å: Chain B: G.133, S.134, I.136, F.237, G.366, I.370 Ligands: FAD.9 Ligand excluded by PLIP GOL.19: 5 residues within 4Å: Chain C: L.5, Y.13, E.74, R.298, Y.302 Ligand excluded by PLIP GOL.20: 4 residues within 4Å: Chain C: Y.13, E.14, Y.17, K.78 Ligand excluded by PLIP GOL.21: 7 residues within 4Å: Chain C: R.81, R.258, L.259, T.262, G.350, L.351, H.354 Ligand excluded by PLIP GOL.22: 7 residues within 4Å: Chain B: K.291, E.295 Chain C: R.303, K.307, A.316, D.317, M.320 Ligand excluded by PLIP GOL.23: 7 residues within 4Å: Chain C: G.133, S.134, I.136, F.237, G.366, I.370 Ligands: FAD.17 Ligand excluded by PLIP GOL.27: 5 residues within 4Å: Chain D: L.5, Y.13, E.74, R.298, Y.302 Ligand excluded by PLIP GOL.28: 4 residues within 4Å: Chain D: Y.13, E.14, Y.17, K.78 Ligand excluded by PLIP GOL.29: 7 residues within 4Å: Chain D: R.81, R.258, L.259, T.262, G.350, L.351, H.354 Ligand excluded by PLIP GOL.30: 7 residues within 4Å: Chain A: K.291, E.295 Chain D: R.303, K.307, A.316, D.317, M.320 Ligand excluded by PLIP GOL.31: 7 residues within 4Å: Chain D: G.133, S.134, I.136, F.237, G.366, I.370 Ligands: FAD.25 Ligand excluded by PLIP

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

CL.8: 3 residues within 4Å: Chain A: Q.281 Chain C: Q.281 Ligands: CL.24 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain B: Q.281 Chain D: Q.281 Ligands: CL.32 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain A: Q.281 Chain C: Q.281 Ligands: CL.8 Ligand excluded by PLIP CL.32: 3 residues within 4Å: Chain B: Q.281 Chain D: Q.281 Ligands: CL.16 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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