SMTL ID : 7poe.1

Phosphoglycolate Phosphatase with Inhibitor CP1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.16 Å

Oligo State

homo-dimer

Ligands

4 x 7VK: 2-[[4-[4-[(2-carboxyphenyl)carbamoyl]phenoxy]phenyl]carbonylamino]benzoic acid(Non-covalent)

7VK.1: 25 residues within 4Å: Chain A: N.34, D.36, N.68, N.69, S.71, G.125, S.126, P.127, V.143, G.144, F.172, P.174, H.175, N.199, D.201, L.204, P.205, I.212, G.214, T.215 Chain B: D.151, G.152, P.153, W.156 Ligands: GOL.3 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:N.68, A:N.69, A:P.127, A:F.172, A:P.174, A:L.204, A:L.204, B:W.156 Hydrogen bonds: A:N.69, A:N.199, A:T.215, A:T.215 pi-Stacking: A:F.172, A:H.175 7VK.2: 20 residues within 4Å: Chain A: M.200, D.201, N.202, R.220, E.223, Q.229, A.230, D.231, I.232, K.235, P.236, S.237, R.261, D.263, T.264 Chain B: E.223, M.224, Q.227, R.228, Q.229 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:M.200, A:N.202, A:I.232, B:Q.227 Hydrogen bonds: A:N.202, A:R.261 Salt bridges: A:R.220 7VK.4: 26 residues within 4Å: Chain A: D.151, G.152, P.153, W.156 Chain B: D.36, N.68, N.69, S.70, S.71, K.72, G.125, S.126, P.127, V.143, G.144, F.172, D.173, P.174, H.175, N.199, D.201, L.204, P.205, I.212, T.215 Ligands: GOL.7 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:N.68, B:N.69, B:P.127, B:F.172, B:P.174, B:L.204, A:W.156 Hydrogen bonds: B:N.69, B:N.199, B:N.199, B:T.215, B:T.215 pi-Stacking: B:F.172 pi-Cation interactions: B:H.175 7VK.5: 17 residues within 4Å: Chain A: E.223, M.224, Q.227, R.228, Q.229 Chain B: M.200, D.201, N.202, R.220, E.223, Q.229, I.232, P.236, S.237, R.261, D.263, T.264 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:M.200, B:N.202 Hydrogen bonds: B:N.202, B:R.261 Salt bridges: B:R.220

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: P.127, V.143, G.144 Ligands: 7VK.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.143 GOL.6: 2 residues within 4Å: Chain B: R.15, Y.308 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.15, B:Y.308, B:Y.308 GOL.7: 6 residues within 4Å: Chain B: S.71, K.72, S.126, P.127, A.128 Ligands: 7VK.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.71

1 x K: POTASSIUM ION(Non-covalent)

K.8: 5 residues within 4Å: Chain B: L.280, G.282, V.283, S.284, S.285 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:G.282

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jeanclos, E. et al., Glycolytic flux control by drugging phosphoglycolate phosphatase. Nat Commun (2022)

Release Date

2022-12-21

Peptides

Glycerol-3-phosphate phosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycerol-3-phosphate phosphatase

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