SMTL ID : 6b7d.1 (4 other biounits)

Crystal structure of E.coli Phosphopantetheine Adenylyltransferase (PPAT/CoaD) in complex with 3-(4-chlorophenyl)-6-methoxy-4,5-dimethylpyridazine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

3 x CWG: 3-(4-chlorophenyl)-6-methoxy-4,5-dimethylpyridazine(Non-covalent)

CWG.1: 13 residues within 4Å: Chain A: A.37, A.38, S.39, F.70, S.71, D.72, L.73, M.74, L.102, M.105 Chain C: L.131, V.135, H.138 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.73, A:M.74, C:H.138 Hydrogen bonds: A:A.38, A:S.39 CWG.12: 13 residues within 4Å: Chain C: A.37, A.38, S.39, F.70, S.71, D.72, L.73, M.74, L.102, M.105 Chain E: L.131, V.135, H.138 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain C Hydrophobic interactions: E:H.138, C:L.73, C:M.74 Hydrogen bonds: C:A.38, C:S.39 CWG.23: 13 residues within 4Å: Chain A: L.131, V.135, H.138 Chain E: A.37, A.38, S.39, F.70, S.71, D.72, L.73, M.74, L.102, M.105 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:L.73, E:M.74, A:H.138 Hydrogen bonds: E:A.38, E:S.39

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

SO4.2: 3 residues within 4Å: Chain A: H.18, S.128, S.129 Ligand excluded by PLIP SO4.3: 4 residues within 4Å: Chain A: S.121, K.122 Chain B: H.104, R.107 Ligand excluded by PLIP SO4.5: 5 residues within 4Å: Chain B: S.39, P.40, S.41 Chain F: R.137, H.138 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain B: H.18, R.91, S.128, S.129 Ligands: K.10 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain A: H.104, R.107 Chain B: S.121, K.122 Ligand excluded by PLIP SO4.8: 5 residues within 4Å: Chain B: G.9, T.10, K.42, R.88 Ligands: K.10 Ligand excluded by PLIP SO4.9: 6 residues within 4Å: Chain B: E.134, V.135 Chain D: L.73, M.74, M.105, N.106 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain C: H.18, S.128, S.129 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain C: S.121, K.122 Chain D: H.104, R.107 Ligand excluded by PLIP SO4.16: 5 residues within 4Å: Chain B: R.137, H.138 Chain D: S.39, P.40, S.41 Ligand excluded by PLIP SO4.17: 5 residues within 4Å: Chain D: H.18, R.91, S.128, S.129 Ligands: K.21 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain C: H.104, R.107 Chain D: S.121, K.122 Ligand excluded by PLIP SO4.19: 5 residues within 4Å: Chain D: G.9, T.10, K.42, R.88 Ligands: K.21 Ligand excluded by PLIP SO4.20: 6 residues within 4Å: Chain D: E.134, V.135 Chain F: L.73, M.74, M.105, N.106 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain E: H.18, S.128, S.129 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain E: S.121, K.122 Chain F: H.104, R.107 Ligand excluded by PLIP SO4.27: 5 residues within 4Å: Chain D: R.137, H.138 Chain F: S.39, P.40, S.41 Ligand excluded by PLIP SO4.28: 5 residues within 4Å: Chain F: H.18, R.91, S.128, S.129 Ligands: K.32 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain E: H.104, R.107 Chain F: S.121, K.122 Ligand excluded by PLIP SO4.30: 5 residues within 4Å: Chain F: G.9, T.10, K.42, R.88 Ligands: K.32 Ligand excluded by PLIP SO4.31: 6 residues within 4Å: Chain B: L.73, M.74, M.105, N.106 Chain F: E.134, V.135 Ligand excluded by PLIP

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

DMS.4: 6 residues within 4Å: Chain A: T.26, Q.27, M.28, F.29, D.30 Chain B: K.3 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.3 Salt bridges: A:D.30 DMS.15: 6 residues within 4Å: Chain C: T.26, Q.27, M.28, F.29, D.30 Chain D: K.3 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:K.3 Salt bridges: C:D.30 DMS.26: 6 residues within 4Å: Chain E: T.26, Q.27, M.28, F.29, D.30 Chain F: K.3 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:K.3 Salt bridges: E:D.30

6 x K: POTASSIUM ION(Non-covalent)

K.10: 5 residues within 4Å: Chain B: T.10, F.11, H.18 Ligands: SO4.6, SO4.8 No protein-ligand interaction detected (PLIP) K.11: 1 residues within 4Å: Chain B: I.21 No protein-ligand interaction detected (PLIP) K.21: 5 residues within 4Å: Chain D: T.10, F.11, H.18 Ligands: SO4.17, SO4.19 No protein-ligand interaction detected (PLIP) K.22: 1 residues within 4Å: Chain D: I.21 No protein-ligand interaction detected (PLIP) K.32: 5 residues within 4Å: Chain F: T.10, F.11, H.18 Ligands: SO4.28, SO4.30 No protein-ligand interaction detected (PLIP) K.33: 1 residues within 4Å: Chain F: I.21 No protein-ligand interaction detected (PLIP)

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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