SMTL ID : 3pxu.1 (1 other biounit)

Crystal structure of phosphopantetheine adenylyltransferase from Burkholderia pseudomallei bound to dephospho-coenzyme A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

6 x COD: DEPHOSPHO COENZYME A(Non-covalent)

COD.1: 27 residues within 4Å: Chain A: Y.10, P.11, G.12, T.13, F.14, G.20, H.21, L.24, A.40, K.45, F.73, G.75, L.76, L.77, R.91, G.92, R.94, Y.101, E.102, M.105, N.109, P.123, Y.127, I.130 Chain C: I.134, E.137, L.141 23 PLIP interactions: 19 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:P.11, A:A.40, C:L.141 Hydrogen bonds: A:Y.10, A:T.13, A:F.14, A:L.77, A:G.92, A:Y.101, A:E.102, A:I.130, C:E.137, C:E.137, C:E.137 Water bridges: A:D.15, A:T.18, A:H.21, A:K.78, A:G.132 Salt bridges: A:H.21, A:K.45, A:R.91 pi-Cation interactions: A:H.21 COD.6: 27 residues within 4Å: Chain A: I.134, E.137, L.141 Chain B: Y.10, P.11, G.12, T.13, F.14, G.20, H.21, L.24, A.40, K.45, F.73, G.75, L.76, L.77, R.91, G.92, R.94, Y.101, E.102, M.105, N.109, P.123, Y.127, I.130 23 PLIP interactions: 3 interactions with chain A, 20 interactions with chain B Hydrophobic interactions: A:L.141, B:P.11, B:A.40 Hydrogen bonds: A:E.137, A:E.137, B:T.13, B:T.13, B:F.14, B:L.77, B:G.92, B:Y.101, B:Y.101, B:E.102, B:E.102, B:I.130 Water bridges: B:D.15, B:H.21, B:K.78, B:G.132 Salt bridges: B:H.21, B:K.45, B:R.91 pi-Cation interactions: B:H.21 COD.11: 27 residues within 4Å: Chain B: I.134, E.137, L.141 Chain C: Y.10, P.11, G.12, T.13, F.14, G.20, H.21, L.24, A.40, K.45, F.73, G.75, L.76, L.77, R.91, G.92, R.94, Y.101, E.102, M.105, N.109, P.123, Y.127, I.130 25 PLIP interactions: 21 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:P.11, C:A.40, B:L.141 Hydrogen bonds: C:Y.10, C:T.13, C:T.13, C:F.14, C:L.77, C:G.92, C:Y.101, C:E.102, C:E.102, C:I.130, B:E.137, B:E.137, B:E.137 Water bridges: C:D.15, C:T.18, C:H.21, C:K.78, C:G.132 Salt bridges: C:H.21, C:K.45, C:R.91 pi-Cation interactions: C:H.21 COD.16: 27 residues within 4Å: Chain D: Y.10, P.11, G.12, T.13, F.14, G.20, H.21, L.24, A.40, K.45, F.73, G.75, L.76, L.77, R.91, G.92, R.94, Y.101, E.102, M.105, N.109, P.123, Y.127, I.130 Chain F: I.134, E.137, L.141 23 PLIP interactions: 20 interactions with chain D, 3 interactions with chain F Hydrophobic interactions: D:P.11, D:A.40, F:L.141 Hydrogen bonds: D:T.13, D:T.13, D:F.14, D:L.77, D:G.92, D:Y.101, D:Y.101, D:E.102, D:E.102, D:I.130, F:E.137, F:E.137 Water bridges: D:D.15, D:H.21, D:K.78, D:G.132 Salt bridges: D:H.21, D:K.45, D:R.91 pi-Cation interactions: D:H.21 COD.21: 27 residues within 4Å: Chain D: I.134, E.137, L.141 Chain E: Y.10, P.11, G.12, T.13, F.14, G.20, H.21, L.24, A.40, K.45, F.73, G.75, L.76, L.77, R.91, G.92, R.94, Y.101, E.102, M.105, N.109, P.123, Y.127, I.130 23 PLIP interactions: 4 interactions with chain D, 19 interactions with chain E Hydrophobic interactions: D:L.141, E:P.11, E:A.40 Hydrogen bonds: D:E.137, D:E.137, D:E.137, E:Y.10, E:T.13, E:F.14, E:L.77, E:G.92, E:Y.101, E:E.102, E:I.130 Water bridges: E:D.15, E:T.18, E:H.21, E:K.78, E:G.132 Salt bridges: E:H.21, E:K.45, E:R.91 pi-Cation interactions: E:H.21 COD.26: 27 residues within 4Å: Chain E: I.134, E.137, L.141 Chain F: Y.10, P.11, G.12, T.13, F.14, G.20, H.21, L.24, A.40, K.45, F.73, G.75, L.76, L.77, R.91, G.92, R.94, Y.101, E.102, M.105, N.109, P.123, Y.127, I.130 21 PLIP interactions: 18 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: F:P.11, F:A.40, E:L.141 Hydrogen bonds: F:T.13, F:F.14, F:L.77, F:G.92, F:Y.101, F:Y.101, F:E.102, F:I.130, E:E.137, E:E.137 Water bridges: F:D.15, F:H.21, F:K.78, F:G.132 Salt bridges: F:H.21, F:K.45, F:R.91 pi-Cation interactions: F:H.21

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: E.22, V.61, H.64, Y.65, F.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.22, A:H.64, A:Y.65 GOL.3: 7 residues within 4Å: Chain A: D.41, R.43, P.47, F.49, S.50, L.51, R.54 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.51, A:R.54, A:R.54 Water bridges: A:S.50, A:E.52 GOL.7: 5 residues within 4Å: Chain B: E.22, V.61, H.64, Y.65, F.150 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.64, B:Y.65 GOL.8: 7 residues within 4Å: Chain B: D.41, R.43, P.47, F.49, S.50, L.51, R.54 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.51, B:R.54, B:R.54 Water bridges: B:S.50, B:E.52 GOL.12: 5 residues within 4Å: Chain C: E.22, V.61, H.64, Y.65, F.150 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.22, C:H.64, C:Y.65 GOL.13: 7 residues within 4Å: Chain C: D.41, R.43, P.47, F.49, S.50, L.51, R.54 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:L.51, C:R.54, C:R.54 Water bridges: C:S.50, C:E.52 GOL.17: 5 residues within 4Å: Chain D: E.22, V.61, H.64, Y.65, F.150 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.64, D:Y.65, D:Y.65 GOL.18: 7 residues within 4Å: Chain D: D.41, R.43, P.47, F.49, S.50, L.51, R.54 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:L.51, D:R.54, D:R.54 Water bridges: D:S.50, D:E.52 GOL.22: 5 residues within 4Å: Chain E: E.22, V.61, H.64, Y.65, F.150 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:E.22, E:H.64, E:Y.65, E:Y.65 GOL.23: 7 residues within 4Å: Chain E: D.41, R.43, P.47, F.49, S.50, L.51, R.54 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:L.51, E:R.54, E:R.54 Water bridges: E:S.50, E:E.52 GOL.27: 5 residues within 4Å: Chain F: E.22, V.61, H.64, Y.65, F.150 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:H.64, F:Y.65, F:Y.65 GOL.28: 7 residues within 4Å: Chain F: D.41, R.43, P.47, F.49, S.50, L.51, R.54 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:L.51, F:R.54, F:R.54 Water bridges: F:S.50, F:E.52

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

SO4.4: 3 residues within 4Å: Chain A: R.19, F.150, P.151 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.19 SO4.5: 5 residues within 4Å: Chain A: R.94, S.131, G.132, T.133 Chain B: Q.104 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.132, A:T.133, A:T.133, B:Q.104 Salt bridges: A:R.94 SO4.9: 3 residues within 4Å: Chain B: R.19, F.150, P.151 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.19 SO4.10: 5 residues within 4Å: Chain B: R.94, S.131, G.132, T.133 Chain C: Q.104 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:G.132, B:T.133, B:T.133, B:T.133, C:Q.104 Salt bridges: B:R.94 SO4.14: 3 residues within 4Å: Chain C: R.19, F.150, P.151 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.19 SO4.15: 5 residues within 4Å: Chain A: Q.104 Chain C: R.94, S.131, G.132, T.133 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:Q.104, C:G.132, C:T.133, C:T.133 Salt bridges: C:R.94 SO4.19: 3 residues within 4Å: Chain D: R.19, F.150, P.151 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.19 SO4.20: 5 residues within 4Å: Chain D: R.94, S.131, G.132, T.133 Chain E: Q.104 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:G.132, D:T.133, D:T.133, D:T.133, E:Q.104 Salt bridges: D:R.94 SO4.24: 3 residues within 4Å: Chain E: R.19, F.150, P.151 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:R.19 SO4.25: 5 residues within 4Å: Chain E: R.94, S.131, G.132, T.133 Chain F: Q.104 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:G.132, E:T.133, E:T.133, F:Q.104 Salt bridges: E:R.94 SO4.29: 3 residues within 4Å: Chain F: R.19, F.150, P.151 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:R.19 SO4.30: 5 residues within 4Å: Chain D: Q.104 Chain F: R.94, S.131, G.132, T.133 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain F Hydrogen bonds: D:Q.104, F:G.132, F:T.133, F:T.133, F:T.133 Salt bridges: F:R.94

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

2010-12-22

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

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