SMTL ID : 6rng.2 (1 other biounit)

Dipeptide Gly-Pro binds to a glycolytic enzyme fructose bisphosphate aldolase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: Q.156, I.159, R.203, A.207 Chain B: K.210, D.214 Chain C: Q.156 7 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B, 2 interactions with chain C Water bridges: A:A.207, B:K.210, B:D.214 Salt bridges: A:R.203, B:K.210 Hydrogen bonds: C:Q.156, C:Q.156 SO4.2: 5 residues within 4Å: Chain A: D.30, E.31, S.32, T.35, K.103 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.32, A:T.35 Water bridges: A:K.142, A:R.144, A:R.144 Salt bridges: A:K.103 SO4.3: 7 residues within 4Å: Chain A: K.210, D.214 Chain B: Q.156, I.159, R.203, A.207 Chain D: Q.156 6 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: D:Q.156, D:Q.156 Water bridges: B:A.207, A:K.210 Salt bridges: B:R.203, A:K.210 SO4.4: 5 residues within 4Å: Chain B: D.30, E.31, S.32, T.35, K.103 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.32 Water bridges: B:K.142, B:R.144, B:R.144 Salt bridges: B:K.103 SO4.5: 7 residues within 4Å: Chain A: Q.156 Chain C: Q.156, I.159, R.203, A.207 Chain D: K.210, D.214 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A, 2 interactions with chain C Water bridges: D:K.210, C:A.207 Salt bridges: D:K.210, C:R.203 Hydrogen bonds: A:Q.156 SO4.6: 5 residues within 4Å: Chain C: D.30, E.31, S.32, T.35, K.103 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.30, C:S.32 Water bridges: C:R.144 Salt bridges: C:K.103 SO4.7: 1 residues within 4Å: Chain C: K.285 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.285 SO4.8: 3 residues within 4Å: Chain C: E.11, K.94, R.139 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:K.94, C:R.139 SO4.13: 7 residues within 4Å: Chain B: Q.156 Chain C: K.210, D.214 Chain D: Q.156, I.159, R.203, A.207 7 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C, 1 interactions with chain B Water bridges: D:A.207, C:K.210, C:D.214, C:D.214 Salt bridges: D:R.203, C:K.210 Hydrogen bonds: B:Q.156 SO4.14: 5 residues within 4Å: Chain D: D.30, E.31, S.32, T.35, K.103 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.30, D:S.32, D:T.35 Water bridges: D:R.144 Salt bridges: D:K.103 SO4.15: 1 residues within 4Å: Chain D: K.285 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:K.285 SO4.16: 3 residues within 4Å: Chain D: E.11, K.94, R.139 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:K.94, D:R.139

4 x GLY: GLYCINE(Non-covalent)

GLY.9: 4 residues within 4Å: Chain C: S.266, G.267, R.298 Ligands: PRO.10 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: C:G.267, C:G.267, P.10 GLY.11: 2 residues within 4Å: Chain C: Y.18 Ligands: PRO.12 No protein-ligand interaction detected (PLIP) GLY.17: 4 residues within 4Å: Chain D: S.266, G.267, R.298 Ligands: PRO.18 3 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain D Hydrogen bonds: P.18, D:G.267, D:G.267 GLY.19: 2 residues within 4Å: Chain D: Y.18 Ligands: PRO.20 No protein-ligand interaction detected (PLIP)

4 x PRO: PROLINE(Non-covalent)

PRO.10: 9 residues within 4Å: Chain C: A.28, E.31, R.39, K.225, S.266, S.295, G.297, R.298 Ligands: GLY.9 8 PLIP interactions: 7 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: C:S.266, C:S.266, C:G.297, C:R.298, P.10 Water bridges: C:K.225 Salt bridges: C:K.142, C:K.225 PRO.12: 4 residues within 4Å: Chain C: N.15, G.97, L.99 Ligands: GLY.11 2 PLIP interactions: 2 interactions with chain C, Hydrophobic interactions: C:L.99 Hydrogen bonds: C:N.15 PRO.18: 9 residues within 4Å: Chain D: A.28, E.31, R.39, K.225, S.266, S.295, G.297, R.298 Ligands: GLY.17 8 PLIP interactions: 7 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: D:S.266, D:S.266, D:G.297, D:R.298, P.18 Water bridges: D:K.225 Salt bridges: D:K.142, D:K.225 PRO.20: 4 residues within 4Å: Chain D: N.15, G.97, L.99 Ligands: GLY.19 2 PLIP interactions: 2 interactions with chain D, Hydrophobic interactions: D:L.99 Hydrogen bonds: D:N.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wojciechowska, I. et al., Dipeptide Gly-Pro binds to a glycolytic enzyme fructose bisphosphate aldolase. Not Published

Release Date

2020-04-15

Peptides

Fructose-bisphosphate aldolase 6, cytosolic: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
F

C
G

D
G

Fructose-bisphosphate aldolase 6, cytosolic

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