SMTL ID : 6b7c.1 (3 other biounits)

Crystal structure of E.coli Phosphopantetheine Adenylyltransferase (PPAT/CoaD) in complex with N-((1,3-dimethyl-1H-pyrazol-5-yl)methyl)-5-methyl-1H-imidazo[4,5-b]pyridin-2-amine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-hexamer

Ligands

6 x CWP: N-[(1,3-dimethyl-1H-pyrazol-5-yl)methyl]-5-methyl-3H-imidazo[4,5-b]pyridin-2-amine(Non-covalent)

CWP.1: 15 residues within 4Å: Chain A: G.9, A.37, F.70, D.72, L.73, M.74, L.102, M.105, N.106 Chain E: L.131, E.134, V.135, H.138 Ligands: DMS.6, SO4.31 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain E Hydrophobic interactions: A:A.37, A:F.70, E:L.131, E:E.134, E:V.135 Hydrogen bonds: A:D.72, A:M.74 Water bridges: A:A.75, E:E.134 pi-Stacking: E:H.138 CWP.7: 17 residues within 4Å: Chain B: P.8, G.9, A.37, S.39, F.70, D.72, L.73, M.74, L.102, M.105, N.106 Chain D: L.131, E.134, V.135, H.138 Ligands: SO4.8, DMS.13 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:P.8, B:A.37, B:F.70, B:L.102, B:M.105, D:L.131, D:E.134 Hydrogen bonds: B:D.72, B:M.74 CWP.15: 15 residues within 4Å: Chain A: L.131, E.134, V.135, H.138 Chain C: G.9, A.37, F.70, D.72, L.73, M.74, L.102, M.105, N.106 Ligands: SO4.3, DMS.20 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:A.37, C:F.70, A:L.131, A:E.134, A:V.135 Hydrogen bonds: C:D.72, C:M.74 Water bridges: C:T.10, C:A.75 pi-Stacking: A:H.138 CWP.21: 17 residues within 4Å: Chain D: P.8, G.9, A.37, S.39, F.70, D.72, L.73, M.74, L.102, M.105, N.106 Chain F: L.131, E.134, V.135, H.138 Ligands: SO4.22, DMS.27 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain F Hydrophobic interactions: D:P.8, D:A.37, D:F.70, D:L.102, D:M.105, F:L.131, F:E.134 Hydrogen bonds: D:D.72, D:M.74 Water bridges: D:T.10 CWP.29: 15 residues within 4Å: Chain C: L.131, E.134, V.135, H.138 Chain E: G.9, A.37, F.70, D.72, L.73, M.74, L.102, M.105, N.106 Ligands: SO4.17, DMS.34 11 PLIP interactions: 6 interactions with chain E, 5 interactions with chain C Hydrophobic interactions: E:A.37, E:F.70, C:L.131, C:E.134, C:V.135 Hydrogen bonds: E:D.72, E:M.74 Water bridges: E:T.10, E:A.75, C:E.134 pi-Stacking: C:H.138 CWP.35: 17 residues within 4Å: Chain B: L.131, E.134, V.135, H.138 Chain F: P.8, G.9, A.37, S.39, F.70, D.72, L.73, M.74, L.102, M.105, N.106 Ligands: SO4.36, DMS.41 9 PLIP interactions: 7 interactions with chain F, 2 interactions with chain B Hydrophobic interactions: F:P.8, F:A.37, F:F.70, F:L.102, F:M.105, B:L.131, B:E.134 Hydrogen bonds: F:D.72, F:M.74

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

SO4.2: 4 residues within 4Å: Chain A: S.121, K.122 Chain B: H.104, R.107 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:K.122 Water bridges: A:R.24, A:S.121, A:K.122, A:E.123, B:H.104, B:H.104 Salt bridges: A:K.122, B:H.104, B:R.107 SO4.3: 6 residues within 4Å: Chain A: E.134, H.138 Chain C: S.39, P.40, S.41 Ligands: CWP.15 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Water bridges: A:E.134 Salt bridges: A:H.138 Hydrogen bonds: C:S.39 SO4.8: 6 residues within 4Å: Chain B: S.39, P.40, S.41 Chain D: R.137, H.138 Ligands: CWP.7 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain B Water bridges: D:E.134, B:S.39 Salt bridges: D:R.137, D:H.138 Hydrogen bonds: B:S.41, B:S.41, B:S.41 SO4.9: 4 residues within 4Å: Chain A: H.104, R.107 Chain B: S.121, K.122 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Salt bridges: A:H.104, A:R.107, B:K.122 Hydrogen bonds: B:S.121, B:K.122 Water bridges: B:R.24, B:E.123 SO4.16: 4 residues within 4Å: Chain C: S.121, K.122 Chain D: H.104, R.107 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:K.122 Water bridges: C:R.24, C:S.121, C:K.122, C:K.122, C:E.123, D:H.104 Salt bridges: C:K.122, D:H.104, D:R.107 SO4.17: 6 residues within 4Å: Chain C: E.134, H.138 Chain E: S.39, P.40, S.41 Ligands: CWP.29 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain E Water bridges: C:E.134, C:E.134 Salt bridges: C:H.138 Hydrogen bonds: E:S.39 SO4.22: 6 residues within 4Å: Chain D: S.39, P.40, S.41 Chain F: R.137, H.138 Ligands: CWP.21 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain F Hydrogen bonds: D:S.41, D:S.41, D:S.41 Water bridges: D:S.39 Salt bridges: F:R.137, F:H.138 SO4.23: 4 residues within 4Å: Chain C: H.104, R.107 Chain D: S.121, K.122 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:S.121, D:K.122 Water bridges: D:R.24, D:E.123 Salt bridges: D:K.122, C:H.104, C:R.107 SO4.30: 4 residues within 4Å: Chain E: S.121, K.122 Chain F: H.104, R.107 10 PLIP interactions: 4 interactions with chain F, 6 interactions with chain E Water bridges: F:H.104, F:H.104, E:R.24, E:S.121, E:K.122, E:E.123 Salt bridges: F:H.104, F:R.107, E:K.122 Hydrogen bonds: E:K.122 SO4.31: 6 residues within 4Å: Chain A: S.39, P.40, S.41 Chain E: E.134, H.138 Ligands: CWP.1 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain A Water bridges: E:E.134, E:E.134 Salt bridges: E:H.138 Hydrogen bonds: A:S.39 SO4.36: 6 residues within 4Å: Chain B: R.137, H.138 Chain F: S.39, P.40, S.41 Ligands: CWP.35 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain F Salt bridges: B:R.137, B:H.138 Hydrogen bonds: F:S.41, F:S.41, F:S.41 Water bridges: F:S.39 SO4.37: 4 residues within 4Å: Chain E: H.104, R.107 Chain F: S.121, K.122 7 PLIP interactions: 5 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:S.121, F:K.122 Water bridges: F:R.24, F:E.123 Salt bridges: F:K.122, E:H.104, E:R.107

9 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 3 residues within 4Å: Chain A: R.4, Q.81, H.82 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.82 PEG.10: 3 residues within 4Å: Chain B: N.16, D.20, W.124 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.20 Water bridges: B:N.16, B:S.121 PEG.11: 2 residues within 4Å: Chain B: R.4, H.82 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.82 PEG.18: 3 residues within 4Å: Chain C: R.4, Q.81, H.82 1 PLIP interactions: 1 interactions with chain C Water bridges: C:H.82 PEG.24: 3 residues within 4Å: Chain D: N.16, D.20, W.124 2 PLIP interactions: 2 interactions with chain D Water bridges: D:N.16, D:S.121 PEG.25: 2 residues within 4Å: Chain D: R.4, H.82 No protein-ligand interaction detected (PLIP) PEG.32: 3 residues within 4Å: Chain E: R.4, Q.81, H.82 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:H.82 PEG.38: 3 residues within 4Å: Chain F: N.16, D.20, W.124 2 PLIP interactions: 2 interactions with chain F Water bridges: F:N.16, F:S.121 PEG.39: 2 residues within 4Å: Chain F: R.4, H.82 No protein-ligand interaction detected (PLIP)

6 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.5: 6 residues within 4Å: Chain A: G.9, T.10, F.11, H.18, S.128, S.129 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:T.10, A:F.11, A:S.129 Water bridges: A:Y.7, A:T.10, A:R.88, A:I.127, A:S.129, A:S.129, A:S.130, A:S.130 Salt bridges: A:H.18, A:H.18 POP.12: 6 residues within 4Å: Chain B: G.9, T.10, F.11, H.18, S.128, S.129 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:T.10, B:F.11, B:S.129 Water bridges: B:T.10, B:H.18, B:H.18, B:R.88, B:S.128, B:S.129, B:S.129, B:S.130 Salt bridges: B:H.18, B:H.18 POP.19: 6 residues within 4Å: Chain C: G.9, T.10, F.11, H.18, S.128, S.129 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:T.10, C:F.11, C:S.129 Water bridges: C:T.10, C:R.88, C:I.127, C:S.129, C:S.129, C:S.130, C:S.130 Salt bridges: C:H.18, C:H.18 POP.26: 6 residues within 4Å: Chain D: G.9, T.10, F.11, H.18, S.128, S.129 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:T.10, D:F.11, D:S.129 Water bridges: D:T.10, D:H.18, D:R.88, D:I.127, D:S.128, D:S.129, D:S.129, D:S.130 Salt bridges: D:H.18, D:H.18 POP.33: 6 residues within 4Å: Chain E: G.9, T.10, F.11, H.18, S.128, S.129 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:T.10, E:F.11, E:S.129 Water bridges: E:Y.7, E:T.10, E:R.88, E:I.127, E:S.129, E:S.129, E:S.130, E:S.130 Salt bridges: E:H.18, E:H.18 POP.40: 6 residues within 4Å: Chain F: G.9, T.10, F.11, H.18, S.128, S.129 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:T.10, F:F.11, F:S.129 Water bridges: F:T.10, F:H.18, F:H.18, F:R.88, F:S.128, F:S.129, F:S.129, F:S.130 Salt bridges: F:H.18, F:H.18

9 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.6: 3 residues within 4Å: Chain A: M.74, Y.98 Ligands: CWP.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.88 DMS.13: 7 residues within 4Å: Chain B: K.42, M.74, R.88, Y.98, L.102 Chain D: E.134 Ligands: CWP.7 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B Salt bridges: D:E.134 Hydrogen bonds: B:R.88, B:R.88 DMS.14: 7 residues within 4Å: Chain A: Q.2 Chain B: T.26, Q.27, M.28, F.29, D.30, N.64 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:D.30 Salt bridges: B:D.30 Hydrogen bonds: A:Q.2 DMS.20: 3 residues within 4Å: Chain C: M.74, Y.98 Ligands: CWP.15 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.88 DMS.27: 7 residues within 4Å: Chain D: K.42, M.74, R.88, Y.98, L.102 Chain F: E.134 Ligands: CWP.21 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain D Salt bridges: F:E.134 Hydrogen bonds: D:R.88, D:R.88 DMS.28: 7 residues within 4Å: Chain C: Q.2 Chain D: T.26, Q.27, M.28, F.29, D.30, N.64 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Water bridges: D:D.30 Salt bridges: D:D.30 Hydrogen bonds: C:Q.2 DMS.34: 3 residues within 4Å: Chain E: M.74, Y.98 Ligands: CWP.29 1 PLIP interactions: 1 interactions with chain E Water bridges: E:R.88 DMS.41: 7 residues within 4Å: Chain B: E.134 Chain F: K.42, M.74, R.88, Y.98, L.102 Ligands: CWP.35 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain F Salt bridges: B:E.134 Hydrogen bonds: F:R.88, F:R.88 DMS.42: 7 residues within 4Å: Chain E: Q.2 Chain F: T.26, Q.27, M.28, F.29, D.30, N.64 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E Water bridges: F:D.30 Salt bridges: F:D.30 Hydrogen bonds: E:Q.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Proudfoot, A. et al., High-Confidence Protein-Ligand Complex Modeling by NMR-Guided Docking Enables Early Hit Optimization. J. Am. Chem. Soc. (2017)

Release Date

2017-12-27

Peptides

Phosphopantetheine adenylyltransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Phosphopantetheine adenylyltransferase

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