SMTL ID : 6b7f.1 (1 other biounit)

Crystal structure of E.coli Phosphopantetheine Adenylyltransferase (PPAT/CoaD) in complex with (R)-3,3-dimethyl-4-(5-vinyl-1H-imidazol-1-yl)isochroman-1-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.56 Å

Oligo State

homo-hexamer

Ligands

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

DMS.1: 7 residues within 4Å: Chain A: G.17, H.18, G.89, R.91, P.120, W.124, I.127 No protein-ligand interaction detected (PLIP) DMS.5: 9 residues within 4Å: Chain B: Y.7, P.8, H.18, R.88, G.89, E.99 Ligands: K.6, SO4.9, SO4.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.7, B:G.89 DMS.11: 7 residues within 4Å: Chain C: G.17, H.18, G.89, R.91, P.120, W.124, I.127 No protein-ligand interaction detected (PLIP) DMS.15: 9 residues within 4Å: Chain D: Y.7, P.8, H.18, R.88, G.89, E.99 Ligands: K.16, SO4.19, SO4.20 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.89 DMS.21: 7 residues within 4Å: Chain E: G.17, H.18, G.89, R.91, P.120, W.124, I.127 No protein-ligand interaction detected (PLIP) DMS.25: 9 residues within 4Å: Chain F: Y.7, P.8, H.18, R.88, G.89, E.99 Ligands: K.26, SO4.29, SO4.30 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:G.89

3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 3 residues within 4Å: Chain A: L.73, M.74, L.102 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.74 TRS.12: 3 residues within 4Å: Chain C: L.73, M.74, L.102 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:M.74 TRS.22: 3 residues within 4Å: Chain E: L.73, M.74, L.102 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:M.74

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

SO4.3: 6 residues within 4Å: Chain A: R.24, P.120, S.121, K.122 Chain B: H.104, R.107 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:H.104, A:R.24, A:K.122 Salt bridges: B:R.107, A:K.122 Water bridges: A:K.122 SO4.8: 5 residues within 4Å: Chain A: H.104, R.107 Chain B: R.24, S.121, K.122 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.24, B:S.121, B:K.122 Water bridges: B:K.122 Salt bridges: B:K.122, A:H.104, A:R.107 SO4.9: 5 residues within 4Å: Chain B: H.18, R.91, S.128, S.129 Ligands: DMS.5 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.129 Water bridges: B:H.18, B:R.91, B:S.129 Salt bridges: B:H.18, B:R.91 SO4.10: 6 residues within 4Å: Chain B: G.9, T.10, K.42, R.88 Ligands: DMS.5, CW4.7 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.10, B:T.10 Water bridges: B:F.11, B:K.42 Salt bridges: B:K.42, B:R.88 SO4.13: 6 residues within 4Å: Chain C: R.24, P.120, S.121, K.122 Chain D: H.104, R.107 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:H.104, C:R.24, C:K.122 Salt bridges: D:R.107, C:K.122 Water bridges: C:K.122 SO4.18: 5 residues within 4Å: Chain C: H.104, R.107 Chain D: R.24, S.121, K.122 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.24, D:S.121, D:K.122 Water bridges: D:K.122 Salt bridges: D:K.122, C:H.104, C:R.107 SO4.19: 5 residues within 4Å: Chain D: H.18, R.91, S.128, S.129 Ligands: DMS.15 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.129 Water bridges: D:H.18, D:R.91, D:S.129 Salt bridges: D:H.18, D:R.91 SO4.20: 6 residues within 4Å: Chain D: G.9, T.10, K.42, R.88 Ligands: DMS.15, CW4.17 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:T.10, D:T.10, D:T.10 Water bridges: D:F.11, D:K.42 Salt bridges: D:K.42, D:R.88 SO4.23: 6 residues within 4Å: Chain E: R.24, P.120, S.121, K.122 Chain F: H.104, R.107 6 PLIP interactions: 2 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:H.104, E:R.24, E:K.122 Salt bridges: F:R.107, E:K.122 Water bridges: E:K.122 SO4.28: 5 residues within 4Å: Chain E: H.104, R.107 Chain F: R.24, S.121, K.122 7 PLIP interactions: 2 interactions with chain E, 5 interactions with chain F Salt bridges: E:H.104, E:R.107, F:K.122 Hydrogen bonds: F:R.24, F:S.121, F:K.122 Water bridges: F:K.122 SO4.29: 5 residues within 4Å: Chain F: H.18, R.91, S.128, S.129 Ligands: DMS.25 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:S.129 Water bridges: F:H.18, F:R.91, F:S.129 Salt bridges: F:H.18, F:R.91 SO4.30: 6 residues within 4Å: Chain F: G.9, T.10, K.42, R.88 Ligands: DMS.25, CW4.27 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:T.10, F:T.10 Water bridges: F:F.11, F:K.42 Salt bridges: F:K.42, F:R.88

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

POP.4: 7 residues within 4Å: Chain A: G.9, T.10, F.11, H.18, R.91, S.128, S.129 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.10, A:F.11, A:S.129 Water bridges: A:Y.7, A:S.129, A:S.129 Salt bridges: A:H.18, A:H.18, A:R.91 POP.14: 7 residues within 4Å: Chain C: G.9, T.10, F.11, H.18, R.91, S.128, S.129 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:T.10, C:T.10, C:F.11, C:S.129 Water bridges: C:S.129, C:S.129 Salt bridges: C:H.18, C:H.18, C:R.91 POP.24: 7 residues within 4Å: Chain E: G.9, T.10, F.11, H.18, R.91, S.128, S.129 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:T.10, E:T.10, E:F.11, E:S.129 Water bridges: E:Y.7, E:S.129, E:S.129 Salt bridges: E:H.18, E:H.18, E:R.91

3 x K: POTASSIUM ION(Non-functional Binders)

K.6: 1 residues within 4Å: Ligands: DMS.5 No protein-ligand interaction detected (PLIP) K.16: 1 residues within 4Å: Ligands: DMS.15 No protein-ligand interaction detected (PLIP) K.26: 1 residues within 4Å: Ligands: DMS.25 No protein-ligand interaction detected (PLIP)

3 x CW4: (4R)-4-(5-ethenyl-1H-imidazol-1-yl)-3,3-dimethyl-3,4-dihydro-1H-2-benzopyran-1-one(Non-covalent)

CW4.7: 12 residues within 4Å: Chain B: A.37, F.70, D.72, L.73, M.74, Y.98, L.102, N.106 Chain D: E.134, V.135, H.138 Ligands: SO4.10 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: D:E.134, D:V.135, B:A.37, B:F.70, B:L.102 Salt bridges: D:H.138 Hydrogen bonds: B:M.74, B:N.106 CW4.17: 12 residues within 4Å: Chain D: A.37, F.70, D.72, L.73, M.74, Y.98, L.102, N.106 Chain F: E.134, V.135, H.138 Ligands: SO4.20 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain F Hydrophobic interactions: D:A.37, D:F.70, D:L.102, F:E.134, F:V.135 Hydrogen bonds: D:M.74, D:N.106 Salt bridges: F:H.138 CW4.27: 12 residues within 4Å: Chain B: E.134, V.135, H.138 Chain F: A.37, F.70, D.72, L.73, M.74, Y.98, L.102, N.106 Ligands: SO4.30 8 PLIP interactions: 5 interactions with chain F, 3 interactions with chain B Hydrophobic interactions: F:A.37, F:F.70, F:L.102, B:E.134, B:V.135 Hydrogen bonds: F:M.74, F:N.106 Salt bridges: B:H.138

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

Related Entries With Identical Sequence