SMTL ID : 6af6.1

PigA with FAD and proline

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 31 residues within 4Å: Chain A: N.125, A.126, A.127, T.128, G.133, S.134, F.158, I.159, T.160, L.206, 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: PRO.5, PRO.6 32 PLIP interactions: 16 interactions with chain A, 12 interactions with chain B, 1 interactions with chain D, 3 Ligand-Ligand interactions Hydrophobic interactions: A:L.206, A:I.363, A:F.364, 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, P.5, P.5, P.6 Water bridges: A:N.368, A:E.373, B:Y.266, B:R.270, B:Q.338, B:G.341, B:A.343 pi-Stacking: A:W.211, B:F.280 Salt bridges: B:R.270, B:R.270 FAD.8: 31 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, L.206, W.211, P.360, I.363, F.364, T.367, D.369, I.370 Chain C: Q.281 Ligands: PRO.12, PRO.13 32 PLIP interactions: 16 interactions with chain B, 12 interactions with chain A, 3 Ligand-Ligand interactions, 1 interactions with chain C Hydrophobic interactions: B:L.206, B:I.363, B:F.364, B:F.364 Hydrogen bonds: 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, A:Q.272, A:R.286, A:Q.338, A:G.342, P.12, P.12, P.13, C:Q.281 Water bridges: B:N.368, B:E.373, A:Y.266, A:R.270, A:Q.338, A:G.341, A:A.343 pi-Stacking: B:W.211, A:F.280 Salt bridges: A:R.270, A:R.270 FAD.15: 31 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, L.206, 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: PRO.19, PRO.20 29 PLIP interactions: 12 interactions with chain D, 16 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:G.341, D:A.343, D:A.343, C:N.368 Salt bridges: D:R.270, D:R.270 pi-Stacking: D:F.280, C:W.211 Hydrophobic interactions: C:L.206, C:I.363, C:F.364, C:F.364 FAD.22: 31 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, L.206, W.211, P.360, I.363, F.364, T.367, D.369, I.370 Ligands: PRO.26, PRO.27 32 PLIP interactions: 3 Ligand-Ligand interactions, 16 interactions with chain D, 12 interactions with chain C, 1 interactions with chain A Hydrogen bonds: P.26, P.26, P.27, 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, C:Q.272, C:R.286, C:Q.338, C:G.342, A:Q.281 Hydrophobic interactions: D:L.206, D:I.363, D:F.364, D:F.364 Water bridges: D:N.368, C:R.270, C:Q.338, C:G.341, C:A.343, C:A.343 pi-Stacking: D:W.211, C:F.280 Salt bridges: C:R.270, C:R.270

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: 5 residues within 4Å: Chain A: F.273, K.275, Q.279, F.280 Ligands: O4B.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.275 O4B.9: 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.10: 5 residues within 4Å: Chain B: F.273, K.275, Q.279, F.280 Ligands: O4B.24 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.275 O4B.16: 3 residues within 4Å: Chain C: E.40, L.41, K.44 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.44 O4B.17: 5 residues within 4Å: Chain C: F.273, K.275, Q.279, F.280 Ligands: O4B.3 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.275 O4B.23: 3 residues within 4Å: Chain D: E.40, L.41, K.44 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.44 O4B.24: 5 residues within 4Å: Chain D: F.273, K.275, Q.279, F.280 Ligands: O4B.10 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.275

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

CL.4: 3 residues within 4Å: Chain A: Q.281 Chain C: Q.281 Ligands: CL.18 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: Q.281 Chain D: Q.281 Ligands: CL.25 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain A: Q.281 Chain C: Q.281 Ligands: CL.4 Ligand excluded by PLIP CL.25: 3 residues within 4Å: Chain B: Q.281 Chain D: Q.281 Ligands: CL.11 Ligand excluded by PLIP

8 x PRO: PROLINE(Non-covalent)

PRO.5: 7 residues within 4Å: Chain A: A.91, N.125, M.241, F.364, S.365 Ligands: FAD.1, PRO.6 3 PLIP interactions: 3 interactions with chain A, Hydrophobic interactions: A:F.364 Hydrogen bonds: A:N.125, A:S.365 PRO.6: 10 residues within 4Å: Chain A: T.128, G.133, S.134, I.136, F.237, S.365, G.366 Ligands: FAD.1, PRO.5, GLY.7 1 PLIP interactions: 1 interactions with chain A, Hydrophobic interactions: A:F.237 PRO.12: 7 residues within 4Å: Chain B: A.91, N.125, M.241, F.364, S.365 Ligands: FAD.8, PRO.13 3 PLIP interactions: 3 interactions with chain B, Hydrophobic interactions: B:F.364 Hydrogen bonds: B:N.125, B:S.365 PRO.13: 10 residues within 4Å: Chain B: T.128, G.133, S.134, I.136, F.237, S.365, G.366 Ligands: FAD.8, PRO.12, GLY.14 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.237 PRO.19: 7 residues within 4Å: Chain C: A.91, N.125, M.241, F.364, S.365 Ligands: FAD.15, PRO.20 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.364 Hydrogen bonds: C:N.125, C:S.365 PRO.20: 10 residues within 4Å: Chain C: T.128, G.133, S.134, I.136, F.237, S.365, G.366 Ligands: FAD.15, PRO.19, GLY.21 1 PLIP interactions: 1 interactions with chain C, Hydrophobic interactions: C:F.237 PRO.26: 7 residues within 4Å: Chain D: A.91, N.125, M.241, F.364, S.365 Ligands: FAD.22, PRO.27 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.364 Hydrogen bonds: D:N.125, D:S.365 PRO.27: 10 residues within 4Å: Chain D: T.128, G.133, S.134, I.136, F.237, S.365, G.366 Ligands: FAD.22, PRO.26, GLY.28 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.237

4 x GLY: GLYCINE(Non-covalent)

GLY.7: 4 residues within 4Å: Chain A: Y.137, H.238, M.241 Ligands: PRO.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.137, A:Y.137 Water bridges: A:H.238, A:K.245, A:K.245 Salt bridges: A:H.238, A:K.245 GLY.14: 4 residues within 4Å: Chain B: Y.137, H.238, M.241 Ligands: PRO.13 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.137, B:Y.137 Water bridges: B:H.238, B:K.245, B:K.245 Salt bridges: B:H.238, B:K.245 GLY.21: 4 residues within 4Å: Chain C: Y.137, H.238, M.241 Ligands: PRO.20 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.137 Water bridges: C:K.245, C:K.245 Salt bridges: C:H.238, C:K.245 GLY.28: 4 residues within 4Å: Chain D: Y.137, H.238, M.241 Ligands: PRO.27 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Y.137 Water bridges: D:K.245, D:K.245 Salt bridges: D:H.238, D:K.245

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