SMTL ID : 3k9w.1

Crystal structure of phosphopantetheine adenylyltransferase from Burkholderia pseudomallei with hydrolyzed 3'-dephospho Coenzyme A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-hexamer

Ligands

6 x 4PS: 4'-diphospho pantetheine(Non-covalent)

4PS.1: 20 residues within 4Å: Chain A: P.28, G.29, T.30, F.31, H.38, A.57, S.59, K.62, F.90, G.92, L.93, L.94, R.108, Y.118, N.126 Chain C: I.151, E.154, I.155, L.158 Ligands: ADE.2 17 PLIP interactions: 13 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:P.28, A:A.57, C:L.158 Hydrogen bonds: A:T.30, A:F.31, A:L.94, A:Y.118, A:Y.118, C:E.154, C:E.154, C:E.154 Water bridges: A:K.95 Salt bridges: A:H.38, A:K.62, A:K.62, A:R.108, A:R.108 4PS.6: 20 residues within 4Å: Chain A: I.151, E.154, I.155, L.158 Chain B: P.28, G.29, T.30, F.31, H.38, A.57, S.59, K.62, F.90, G.92, L.93, L.94, R.108, Y.118, N.126 Ligands: ADE.7 17 PLIP interactions: 14 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:P.28, B:A.57, A:L.158 Hydrogen bonds: B:T.30, B:T.30, B:F.31, B:L.94, B:Y.118, B:Y.118, A:E.154, A:E.154 Water bridges: B:K.95 Salt bridges: B:H.38, B:K.62, B:K.62, B:R.108, B:R.108 4PS.11: 20 residues within 4Å: Chain B: I.151, E.154, I.155, L.158 Chain C: P.28, G.29, T.30, F.31, H.38, A.57, S.59, K.62, F.90, G.92, L.93, L.94, R.108, Y.118, N.126 Ligands: ADE.12 17 PLIP interactions: 14 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:P.28, C:A.57, B:L.158 Hydrogen bonds: C:T.30, C:T.30, C:F.31, C:L.94, C:Y.118, C:Y.118, B:E.154, B:E.154 Water bridges: C:K.95 Salt bridges: C:H.38, C:K.62, C:K.62, C:R.108, C:R.108 4PS.16: 20 residues within 4Å: Chain D: P.28, G.29, T.30, F.31, H.38, A.57, S.59, K.62, F.90, G.92, L.93, L.94, R.108, Y.118, N.126 Chain F: I.151, E.154, I.155, L.158 Ligands: ADE.17 17 PLIP interactions: 14 interactions with chain D, 3 interactions with chain F Hydrophobic interactions: D:P.28, D:A.57, F:L.158 Hydrogen bonds: D:T.30, D:T.30, D:F.31, D:L.94, D:Y.118, D:Y.118, F:E.154, F:E.154 Water bridges: D:K.95 Salt bridges: D:H.38, D:K.62, D:K.62, D:R.108, D:R.108 4PS.21: 20 residues within 4Å: Chain D: I.151, E.154, I.155, L.158 Chain E: P.28, G.29, T.30, F.31, H.38, A.57, S.59, K.62, F.90, G.92, L.93, L.94, R.108, Y.118, N.126 Ligands: ADE.22 17 PLIP interactions: 13 interactions with chain E, 4 interactions with chain D Hydrophobic interactions: E:P.28, E:A.57, D:L.158 Hydrogen bonds: E:T.30, E:F.31, E:L.94, E:Y.118, E:Y.118, D:E.154, D:E.154, D:E.154 Water bridges: E:K.95 Salt bridges: E:H.38, E:K.62, E:K.62, E:R.108, E:R.108 4PS.26: 20 residues within 4Å: Chain E: I.151, E.154, I.155, L.158 Chain F: P.28, G.29, T.30, F.31, H.38, A.57, S.59, K.62, F.90, G.92, L.93, L.94, R.108, Y.118, N.126 Ligands: ADE.27 17 PLIP interactions: 13 interactions with chain F, 4 interactions with chain E Hydrophobic interactions: F:P.28, F:A.57, E:L.158 Hydrogen bonds: F:T.30, F:F.31, F:L.94, F:Y.118, F:Y.118, E:E.154, E:E.154, E:E.154 Water bridges: F:K.95 Salt bridges: F:H.38, F:K.62, F:K.62, F:R.108, F:R.108

6 x ADE: ADENINE(Non-covalent)

ADE.2: 10 residues within 4Å: Chain A: Y.27, G.37, H.38, R.111, P.140, Y.144, I.147 Ligands: 4PS.1, ACT.4, SO4.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.27, A:R.111, A:I.147 Water bridges: A:T.35, A:G.109, A:G.109, A:G.149 pi-Cation interactions: A:H.38, A:R.111 ADE.7: 10 residues within 4Å: Chain B: Y.27, G.37, H.38, R.111, P.140, Y.144, I.147 Ligands: 4PS.6, ACT.9, SO4.10 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.111, B:I.147 Water bridges: B:G.109, B:G.109, B:G.149 pi-Cation interactions: B:H.38, B:R.111 ADE.12: 10 residues within 4Å: Chain C: Y.27, G.37, H.38, R.111, P.140, Y.144, I.147 Ligands: 4PS.11, ACT.14, SO4.15 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:Y.27, C:R.111, C:I.147 Water bridges: C:T.35, C:G.109, C:G.109, C:G.149 pi-Cation interactions: C:H.38, C:R.111 ADE.17: 10 residues within 4Å: Chain D: Y.27, G.37, H.38, R.111, P.140, Y.144, I.147 Ligands: 4PS.16, ACT.19, SO4.20 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.111, D:I.147 Water bridges: D:G.109, D:G.109, D:G.149 pi-Cation interactions: D:H.38, D:R.111 ADE.22: 10 residues within 4Å: Chain E: Y.27, G.37, H.38, R.111, P.140, Y.144, I.147 Ligands: 4PS.21, ACT.24, SO4.25 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:Y.27, E:R.111, E:I.147 Water bridges: E:T.35, E:G.109, E:G.109, E:G.149 pi-Cation interactions: E:H.38, E:R.111 ADE.27: 10 residues within 4Å: Chain F: Y.27, G.37, H.38, R.111, P.140, Y.144, I.147 Ligands: 4PS.26, ACT.29, SO4.30 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:R.111, F:I.147 Water bridges: F:G.109, F:G.109, F:G.149 pi-Cation interactions: F:H.38, F:R.111

6 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 7 residues within 4Å: Chain A: D.58, P.64, F.66, S.67, L.68, E.69, R.71 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.58, A:L.68, A:E.69, A:E.69, A:R.71 PG4.8: 7 residues within 4Å: Chain B: D.58, P.64, F.66, S.67, L.68, E.69, R.71 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.58, B:L.68, B:E.69, B:E.69, B:E.69, B:R.71 PG4.13: 7 residues within 4Å: Chain C: D.58, P.64, F.66, S.67, L.68, E.69, R.71 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.58, C:L.68, C:E.69, C:E.69, C:R.71 PG4.18: 7 residues within 4Å: Chain D: D.58, P.64, F.66, S.67, L.68, E.69, R.71 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:D.58, D:L.68, D:E.69, D:E.69, D:E.69, D:R.71 PG4.23: 7 residues within 4Å: Chain E: D.58, P.64, F.66, S.67, L.68, E.69, R.71 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:D.58, E:L.68, E:E.69, E:E.69, E:R.71 PG4.28: 7 residues within 4Å: Chain F: D.58, P.64, F.66, S.67, L.68, E.69, R.71 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:D.58, F:L.68, F:E.69, F:E.69, F:E.69, F:R.71

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

ACT.4: 5 residues within 4Å: Chain A: S.148, G.149, T.150 Chain B: Q.121 Ligands: ADE.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.149, A:T.150 ACT.9: 5 residues within 4Å: Chain B: S.148, G.149, T.150 Chain C: Q.121 Ligands: ADE.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.149, B:T.150, B:T.150 ACT.14: 5 residues within 4Å: Chain A: Q.121 Chain C: S.148, G.149, T.150 Ligands: ADE.12 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.149, C:T.150 ACT.19: 5 residues within 4Å: Chain D: S.148, G.149, T.150 Chain E: Q.121 Ligands: ADE.17 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.149, D:T.150, D:T.150 ACT.24: 5 residues within 4Å: Chain E: S.148, G.149, T.150 Chain F: Q.121 Ligands: ADE.22 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:G.149, E:T.150 ACT.29: 5 residues within 4Å: Chain D: Q.121 Chain F: S.148, G.149, T.150 Ligands: ADE.27 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:G.149, F:T.150, F:T.150

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

SO4.5: 7 residues within 4Å: Chain A: R.111, S.114, D.115, Y.118, E.119 Chain B: E.117 Ligands: ADE.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.115 Salt bridges: A:R.111 SO4.10: 7 residues within 4Å: Chain B: R.111, S.114, D.115, Y.118, E.119 Chain C: E.117 Ligands: ADE.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.115, B:E.119 Salt bridges: B:R.111 SO4.15: 7 residues within 4Å: Chain A: E.117 Chain C: R.111, S.114, D.115, Y.118, E.119 Ligands: ADE.12 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.115, C:E.119 Salt bridges: C:R.111 SO4.20: 7 residues within 4Å: Chain D: R.111, S.114, D.115, Y.118, E.119 Chain E: E.117 Ligands: ADE.17 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.115, D:E.119 Salt bridges: D:R.111 SO4.25: 7 residues within 4Å: Chain E: R.111, S.114, D.115, Y.118, E.119 Chain F: E.117 Ligands: ADE.22 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.115 Salt bridges: E:R.111 SO4.30: 7 residues within 4Å: Chain D: E.117 Chain F: R.111, S.114, D.115, Y.118, E.119 Ligands: ADE.27 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:D.115 Salt bridges: F:R.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Edwards, T.E. et al., Structures of phosphopantetheine adenylyltransferase from Burkholderia pseudomallei. Acta Crystallogr.,Sect.F (2011)

Release Date

2009-11-03

Peptides

Phosphopantetheine adenylyltransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Phosphopantetheine adenylyltransferase