SMTL ID : 6b7a.1 (4 other biounits)

Crystal structure of E.coli Phosphopantetheine Adenylyltransferase (PPAT/CoaD) in complex with 2-methyl-1H-benzo[d]imidazol-4-ol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-hexamer

Ligands

6 x CWM: 2-methyl-1H-benzimidazol-7-ol(Non-covalent)

CWM.1: 7 residues within 4Å: Chain A: L.73, M.74, A.75, M.105, N.106 Chain C: E.134, V.135 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:M.74, A:A.75, A:N.106, A:N.106 Hydrophobic interactions: C:E.134, C:V.135 CWM.7: 10 residues within 4Å: Chain B: D.72, L.73, M.74, A.75, M.105, N.106, L.109 Chain F: E.134, V.135, H.138 7 PLIP interactions: 3 interactions with chain F, 4 interactions with chain B Hydrophobic interactions: F:E.134, F:V.135, B:L.109 Hydrogen bonds: F:E.134, B:M.74, B:A.75, B:N.106 CWM.13: 7 residues within 4Å: Chain C: L.73, M.74, A.75, M.105, N.106 Chain E: E.134, V.135 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain E Hydrogen bonds: C:M.74, C:A.75, C:N.106, C:N.106 Hydrophobic interactions: E:E.134, E:V.135 CWM.19: 10 residues within 4Å: Chain B: E.134, V.135, H.138 Chain D: D.72, L.73, M.74, A.75, M.105, N.106, L.109 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:E.134, B:V.135, D:L.109 Hydrogen bonds: D:M.74, D:A.75, D:N.106 CWM.25: 7 residues within 4Å: Chain A: E.134, V.135 Chain E: L.73, M.74, A.75, M.105, N.106 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain E Hydrophobic interactions: A:E.134, A:V.135 Hydrogen bonds: E:M.74, E:A.75, E:N.106, E:N.106 CWM.31: 10 residues within 4Å: Chain D: E.134, V.135, H.138 Chain F: D.72, L.73, M.74, A.75, M.105, N.106, L.109 6 PLIP interactions: 4 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: F:L.109, D:E.134, D:V.135 Hydrogen bonds: F:M.74, F:A.75, F:N.106

15 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 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Water bridges: B:H.104, A:R.24, A:R.24, A:K.122 Salt bridges: B:H.104, B:R.107, A:K.122 Hydrogen bonds: A:K.122 SO4.3: 5 residues within 4Å: Chain A: H.18, R.91, S.128, S.129 Ligands: PEG.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.129 Water bridges: A:H.18, A:R.91, A:S.129, A:S.130 Salt bridges: A:H.18, A:R.91 SO4.8: 5 residues within 4Å: Chain B: S.39, P.40, S.41 Chain F: R.137, H.138 6 PLIP interactions: 4 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:E.134, B:S.41 Water bridges: F:H.138, B:S.39 Salt bridges: F:R.137, F:H.138 SO4.9: 6 residues within 4Å: Chain A: Q.2 Chain B: T.26, Q.27, M.28, F.29, D.30 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.2, B:Q.27, B:D.30, B:D.30 Salt bridges: A:K.3 SO4.10: 4 residues within 4Å: Chain A: H.104, R.107 Chain B: S.121, K.122 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.24, B:S.121, B:K.122 Salt bridges: B:K.122, A:H.104, A:R.107 Water bridges: A:H.104, A:H.104 SO4.14: 4 residues within 4Å: Chain C: S.121, K.122 Chain D: H.104, R.107 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:K.122 Water bridges: C:R.24, C:R.24, C:K.122, D:H.104 Salt bridges: C:K.122, D:H.104, D:R.107 SO4.15: 5 residues within 4Å: Chain C: H.18, R.91, S.128, S.129 Ligands: PEG.17 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.129 Water bridges: C:R.91, C:S.129, C:S.130 Salt bridges: C:H.18, C:R.91 SO4.20: 5 residues within 4Å: Chain B: R.137, H.138 Chain D: S.39, P.40, S.41 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Water bridges: B:H.138, D:S.39 Salt bridges: B:R.137, B:H.138 Hydrogen bonds: D:S.41 SO4.21: 6 residues within 4Å: Chain C: Q.2 Chain D: T.26, Q.27, M.28, F.29, D.30 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.2, D:Q.27, D:D.30 Salt bridges: C:K.3 SO4.22: 4 residues within 4Å: Chain C: H.104, R.107 Chain D: S.121, K.122 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:R.24, D:S.121, D:K.122 Water bridges: D:K.122, C:H.104 Salt bridges: D:K.122, C:H.104, C:R.107 SO4.26: 4 residues within 4Å: Chain E: S.121, K.122 Chain F: H.104, R.107 8 PLIP interactions: 3 interactions with chain F, 5 interactions with chain E Water bridges: F:H.104, E:R.24, E:R.24, E:K.122 Salt bridges: F:H.104, F:R.107, E:K.122 Hydrogen bonds: E:K.122 SO4.27: 5 residues within 4Å: Chain E: H.18, R.91, S.128, S.129 Ligands: PEG.29 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:S.129 Water bridges: E:R.91, E:S.129, E:S.130 Salt bridges: E:H.18, E:R.91 SO4.32: 5 residues within 4Å: Chain D: R.137, H.138 Chain F: S.39, P.40, S.41 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain F Water bridges: D:H.138, F:S.39 Salt bridges: D:R.137, D:H.138 Hydrogen bonds: F:S.41 SO4.33: 6 residues within 4Å: Chain E: Q.2 Chain F: T.26, Q.27, M.28, F.29, D.30 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:Q.27, F:D.30, F:D.30, E:Q.2 Salt bridges: E:K.3 SO4.34: 4 residues within 4Å: Chain E: H.104, R.107 Chain F: S.121, K.122 8 PLIP interactions: 3 interactions with chain E, 5 interactions with chain F Water bridges: E:H.104, F:K.122 Salt bridges: E:H.104, E:R.107, F:K.122 Hydrogen bonds: F:R.24, F:S.121, F:K.122

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.5: 5 residues within 4Å: Chain A: Y.7, I.21, R.88, G.89 Ligands: SO4.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.7, A:G.89 Water bridges: A:H.18, A:H.18, A:R.88, A:R.91 PEG.11: 6 residues within 4Å: Chain B: Y.7, P.8, G.9, R.88, G.89 Ligands: POP.12 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.7, B:P.8, B:G.89 Water bridges: B:I.127 PEG.16: 3 residues within 4Å: Chain C: R.4, Q.81, H.82 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.82 PEG.17: 5 residues within 4Å: Chain C: Y.7, I.21, R.88, G.89 Ligands: SO4.15 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.7, C:G.89 Water bridges: C:R.88, C:R.91 PEG.23: 6 residues within 4Å: Chain D: Y.7, P.8, G.9, R.88, G.89 Ligands: POP.24 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:P.8, D:G.89 Water bridges: D:I.127 PEG.28: 3 residues within 4Å: Chain E: R.4, Q.81, H.82 No protein-ligand interaction detected (PLIP) PEG.29: 5 residues within 4Å: Chain E: Y.7, I.21, R.88, G.89 Ligands: SO4.27 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:G.89 Water bridges: E:R.88, E:R.91 PEG.35: 6 residues within 4Å: Chain F: Y.7, P.8, G.9, R.88, G.89 Ligands: POP.36 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:P.8, F:G.89 Water bridges: F:I.127

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

CL.6: 3 residues within 4Å: Chain A: H.138 Chain E: P.40, S.41 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain A: P.40, S.41 Chain C: H.138 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain C: P.40, S.41 Chain E: H.138 Ligand excluded by PLIP

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

POP.12: 8 residues within 4Å: Chain B: G.9, T.10, F.11, H.18, R.91, S.128, S.129 Ligands: PEG.11 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:T.10, B:F.11, B:S.129 Water bridges: B:D.12, B:K.42, B:S.129, B:S.130 Salt bridges: B:H.18, B:H.18, B:R.91 POP.24: 8 residues within 4Å: Chain D: G.9, T.10, F.11, H.18, R.91, S.128, S.129 Ligands: PEG.23 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:T.10, D:F.11, D:S.129 Water bridges: D:D.12, D:K.42, D:S.129, D:S.130 Salt bridges: D:H.18, D:H.18, D:R.91 POP.36: 8 residues within 4Å: Chain F: G.9, T.10, F.11, H.18, R.91, S.128, S.129 Ligands: PEG.35 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:T.10, F:F.11, F:S.129 Water bridges: F:T.10, F:D.12, F:K.42, F:S.129, F:S.130 Salt bridges: F:H.18, F:H.18, F:R.91

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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