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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

14 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 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: A:Q.156, C:Q.156 Salt bridges: A:R.203, B:K.210 Water bridges: B:K.210 SO4.2: 1 residues within 4Å: Chain A: R.253 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.202 Salt bridges: A:R.253 SO4.3: 5 residues within 4Å: Chain A: D.30, S.32, T.35, K.103, K.142 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.30, A:S.32, A:T.35 Salt bridges: A:K.103, A:K.142 SO4.4: 1 residues within 4Å: Chain A: K.285 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.285 SO4.5: 3 residues within 4Å: Chain A: E.11, K.94, R.139 4 PLIP interactions: 4 interactions with chain A Water bridges: A:E.11, A:K.94 Salt bridges: A:K.94, A:R.139 SO4.6: 4 residues within 4Å: Chain A: Q.156, R.203 Chain C: Q.156, R.203 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:Q.156, C:Q.156, C:Q.156 Salt bridges: A:R.203, C:R.203 SO4.9: 7 residues within 4Å: Chain A: K.210, D.214 Chain B: Q.156, I.159, R.203, A.207 Chain D: Q.156 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 1 interactions with chain D Water bridges: A:K.210 Salt bridges: A:K.210, B:R.203 Hydrogen bonds: B:Q.156, D:Q.156 SO4.10: 1 residues within 4Å: Chain B: R.253 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.202 Salt bridges: B:R.253 SO4.11: 5 residues within 4Å: Chain B: D.30, S.32, T.35, K.103, K.142 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.30, B:S.32 Salt bridges: B:K.103, B:K.142 SO4.12: 1 residues within 4Å: Chain B: K.285 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.285 SO4.13: 3 residues within 4Å: Chain B: E.11, K.94, R.139 4 PLIP interactions: 4 interactions with chain B Water bridges: B:E.11, B:K.94 Salt bridges: B:K.94, B:R.139 SO4.14: 4 residues within 4Å: Chain B: Q.156, R.203 Chain D: Q.156, R.203 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:Q.156, D:Q.156, D:Q.156 Salt bridges: B:R.203, D:R.203 SO4.17: 5 residues within 4Å: Chain C: Q.156, I.159, R.203 Chain D: K.210, D.214 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Salt bridges: C:R.203, D:K.210 SO4.18: 5 residues within 4Å: Chain C: K.210, D.214 Chain D: Q.156, I.159, R.203 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Salt bridges: C:K.210, D:R.203

2 x GLY: GLYCINE(Non-covalent)

GLY.7: 4 residues within 4Å: Chain A: S.266, G.267, R.298 Ligands: PRO.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.266, A:G.267 GLY.15: 4 residues within 4Å: Chain B: S.266, G.267, R.298 Ligands: PRO.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.266, B:G.267

2 x PRO: PROLINE(Non-covalent)

PRO.8: 6 residues within 4Å: Chain A: L.265, S.266, G.267, S.295, R.298 Ligands: GLY.7 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:S.266, A:G.267, A:S.295, A:G.297 Water bridges: A:R.298, P.8 Salt bridges: A:K.225 PRO.16: 6 residues within 4Å: Chain B: L.265, S.266, G.267, S.295, R.298 Ligands: GLY.15 7 PLIP interactions: 6 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:S.266, B:G.267, B:S.295, B:G.297 Water bridges: B:R.298, P.16 Salt bridges: B:K.225

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
B

B
B

C
A

D
A

Fructose-bisphosphate aldolase 6, cytosolic

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