SMTL ID : 3r1m.1

Structure of bifunctional fructose 1,6-bisphosphate aldolase/phosphatase (aldolase form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-octamer

Ligands

8 x 13P: 1,3-DIHYDROXYACETONEPHOSPHATE(Covalent)

13P.1: 17 residues within 4Å: Chain A: D.12, H.19, D.53, Q.95, D.132, K.133, Y.229, G.231, K.232, D.234, W.264, M.265, R.266, D.287 Ligands: MG.2, MG.3, MG.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:K.232 Hydrogen bonds: A:Q.95, A:K.232, A:R.266 Water bridges: A:H.19, A:D.234, A:D.234, A:D.287 Salt bridges: A:H.19, A:K.133, A:K.232 13P.6: 17 residues within 4Å: Chain B: D.12, H.19, D.53, Q.95, D.132, K.133, Y.229, G.231, K.232, D.234, W.264, M.265, R.266, D.287 Ligands: MG.7, MG.8, MG.9 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:K.232 Hydrogen bonds: B:Q.95, B:K.232, B:R.266 Water bridges: B:H.19, B:D.234, B:D.234, B:D.287 Salt bridges: B:H.19, B:K.133, B:K.232 13P.11: 17 residues within 4Å: Chain C: D.12, H.19, D.53, Q.95, D.132, K.133, Y.229, G.231, K.232, D.234, W.264, M.265, R.266, D.287 Ligands: MG.12, MG.13, MG.14 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:K.232 Hydrogen bonds: C:Q.95, C:K.232, C:R.266 Water bridges: C:H.19, C:D.234, C:D.234, C:D.287 Salt bridges: C:H.19, C:K.133, C:K.232 13P.16: 17 residues within 4Å: Chain D: D.12, H.19, D.53, Q.95, D.132, K.133, Y.229, G.231, K.232, D.234, W.264, M.265, R.266, D.287 Ligands: MG.17, MG.18, MG.19 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:K.232 Hydrogen bonds: D:Q.95, D:K.232, D:R.266 Water bridges: D:H.19, D:D.234, D:D.234, D:D.287 Salt bridges: D:H.19, D:K.133, D:K.232 13P.21: 17 residues within 4Å: Chain E: D.12, H.19, D.53, Q.95, D.132, K.133, Y.229, G.231, K.232, D.234, W.264, M.265, R.266, D.287 Ligands: MG.22, MG.23, MG.24 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:K.232 Hydrogen bonds: E:D.12, E:Q.95, E:K.232, E:K.232, E:R.266, E:D.287 Water bridges: E:H.19, E:Y.229, E:D.287 Salt bridges: E:H.19, E:K.133, E:K.232 13P.26: 17 residues within 4Å: Chain F: D.12, H.19, D.53, Q.95, D.132, K.133, Y.229, G.231, K.232, D.234, W.264, M.265, R.266, D.287 Ligands: MG.27, MG.28, MG.29 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:K.232 Hydrogen bonds: F:D.12, F:Q.95, F:K.232, F:K.232, F:R.266, F:D.287 Water bridges: F:H.19, F:Y.229, F:D.287 Salt bridges: F:H.19, F:K.133, F:K.232 13P.31: 17 residues within 4Å: Chain G: D.12, H.19, D.53, Q.95, D.132, K.133, Y.229, G.231, K.232, D.234, W.264, M.265, R.266, D.287 Ligands: MG.32, MG.33, MG.34 13 PLIP interactions: 13 interactions with chain G Hydrophobic interactions: G:K.232 Hydrogen bonds: G:D.12, G:Q.95, G:K.232, G:K.232, G:R.266, G:D.287 Water bridges: G:H.19, G:Y.229, G:D.287 Salt bridges: G:H.19, G:K.133, G:K.232 13P.36: 17 residues within 4Å: Chain H: D.12, H.19, D.53, Q.95, D.132, K.133, Y.229, G.231, K.232, D.234, W.264, M.265, R.266, D.287 Ligands: MG.37, MG.38, MG.39 13 PLIP interactions: 13 interactions with chain H Hydrophobic interactions: H:K.232 Hydrogen bonds: H:D.12, H:Q.95, H:K.232, H:K.232, H:R.266, H:D.287 Water bridges: H:H.19, H:Y.229, H:D.287 Salt bridges: H:H.19, H:K.133, H:K.232

24 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.54, K.232, D.234 Ligands: 13P.1, MG.3 6 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:K.232, A:D.234, H2O.1, H2O.1, H2O.1, 13P.1 MG.3: 7 residues within 4Å: Chain A: D.53, D.54, D.132, K.133, D.234 Ligands: 13P.1, MG.2 6 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.53, A:D.54, A:D.132, A:D.234, H2O.1, 13P.1 MG.4: 5 residues within 4Å: Chain A: D.12, H.19, D.53, Q.95 Ligands: 13P.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.12, A:H.19, A:D.53, H2O.1 MG.7: 5 residues within 4Å: Chain B: D.54, K.232, D.234 Ligands: 13P.6, MG.8 6 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: B:K.232, B:D.234, 13P.6, H2O.11, H2O.11, H2O.11 MG.8: 7 residues within 4Å: Chain B: D.53, D.54, D.132, K.133, D.234 Ligands: 13P.6, MG.7 6 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:D.53, B:D.54, B:D.132, B:D.234, 13P.6, H2O.11 MG.9: 5 residues within 4Å: Chain B: D.12, H.19, D.53, Q.95 Ligands: 13P.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.12, B:H.19, B:D.53, H2O.11 MG.12: 5 residues within 4Å: Chain C: D.54, K.232, D.234 Ligands: 13P.11, MG.13 6 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: C:K.232, C:D.234, 13P.11, H2O.21, H2O.21, H2O.21 MG.13: 7 residues within 4Å: Chain C: D.53, D.54, D.132, K.133, D.234 Ligands: 13P.11, MG.12 6 PLIP interactions: 4 interactions with chain C, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: C:D.53, C:D.54, C:D.132, C:D.234, 13P.11, H2O.21 MG.14: 5 residues within 4Å: Chain C: D.12, H.19, D.53, Q.95 Ligands: 13P.11 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.12, C:H.19, C:D.53, H2O.21 MG.17: 5 residues within 4Å: Chain D: D.54, K.232, D.234 Ligands: 13P.16, MG.18 6 PLIP interactions: 2 interactions with chain D, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: D:K.232, D:D.234, 13P.16, H2O.31, H2O.31, H2O.31 MG.18: 7 residues within 4Å: Chain D: D.53, D.54, D.132, K.133, D.234 Ligands: 13P.16, MG.17 6 PLIP interactions: 4 interactions with chain D, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: D:D.53, D:D.54, D:D.132, D:D.234, 13P.16, H2O.31 MG.19: 5 residues within 4Å: Chain D: D.12, H.19, D.53, Q.95 Ligands: 13P.16 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.12, D:H.19, D:D.53, H2O.31 MG.22: 5 residues within 4Å: Chain E: D.54, K.232, D.234 Ligands: 13P.21, MG.23 6 PLIP interactions: 2 interactions with chain E, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: E:K.232, E:D.234, 13P.21, H2O.41, H2O.41, H2O.41 MG.23: 7 residues within 4Å: Chain E: D.53, D.54, D.132, K.133, D.234 Ligands: 13P.21, MG.22 6 PLIP interactions: 4 interactions with chain E, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: E:D.53, E:D.54, E:D.132, E:D.234, 13P.21, H2O.41 MG.24: 5 residues within 4Å: Chain E: D.12, H.19, D.53, Q.95 Ligands: 13P.21 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.12, E:H.19, E:D.53, H2O.41 MG.27: 5 residues within 4Å: Chain F: D.54, K.232, D.234 Ligands: 13P.26, MG.28 6 PLIP interactions: 2 interactions with chain F, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: F:K.232, F:D.234, 13P.26, H2O.51, H2O.51, H2O.51 MG.28: 7 residues within 4Å: Chain F: D.53, D.54, D.132, K.133, D.234 Ligands: 13P.26, MG.27 6 PLIP interactions: 4 interactions with chain F, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: F:D.53, F:D.54, F:D.132, F:D.234, 13P.26, H2O.51 MG.29: 5 residues within 4Å: Chain F: D.12, H.19, D.53, Q.95 Ligands: 13P.26 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.12, F:H.19, F:D.53, H2O.51 MG.32: 5 residues within 4Å: Chain G: D.54, K.232, D.234 Ligands: 13P.31, MG.33 6 PLIP interactions: 2 interactions with chain G, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: G:K.232, G:D.234, 13P.31, H2O.61, H2O.62, H2O.62 MG.33: 7 residues within 4Å: Chain G: D.53, D.54, D.132, K.133, D.234 Ligands: 13P.31, MG.32 6 PLIP interactions: 4 interactions with chain G, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: G:D.53, G:D.54, G:D.132, G:D.234, 13P.31, H2O.61 MG.34: 5 residues within 4Å: Chain G: D.12, H.19, D.53, Q.95 Ligands: 13P.31 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.12, G:H.19, G:D.53, H2O.61 MG.37: 5 residues within 4Å: Chain H: D.54, K.232, D.234 Ligands: 13P.36, MG.38 6 PLIP interactions: 2 interactions with chain H, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: H:K.232, H:D.234, 13P.36, H2O.72, H2O.72, H2O.72 MG.38: 7 residues within 4Å: Chain H: D.53, D.54, D.132, K.133, D.234 Ligands: 13P.36, MG.37 6 PLIP interactions: 4 interactions with chain H, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: H:D.53, H:D.54, H:D.132, H:D.234, 13P.36, H2O.72 MG.39: 5 residues within 4Å: Chain H: D.12, H.19, D.53, Q.95 Ligands: 13P.36 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.12, H:H.19, H:D.53, H2O.72

8 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.5: 5 residues within 4Å: Chain A: G.306, P.307 Chain C: L.16, H.23, P.24 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.16, C:P.24 Water bridges: C:H.23 Hydrogen bonds: A:G.306 MPD.10: 5 residues within 4Å: Chain B: G.306, P.307 Chain D: L.16, H.23, P.24 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:L.16, D:P.24 Water bridges: D:H.23 Hydrogen bonds: B:G.306 MPD.15: 5 residues within 4Å: Chain B: L.16, H.23, P.24 Chain C: G.306, P.307 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:G.306 Hydrophobic interactions: B:L.16, B:P.24 Water bridges: B:H.23 MPD.20: 5 residues within 4Å: Chain A: L.16, H.23, P.24 Chain D: G.306, P.307 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:L.16, A:P.24 Water bridges: A:H.23 Hydrogen bonds: D:G.306 MPD.25: 5 residues within 4Å: Chain E: G.306, P.307 Chain G: L.16, H.23, P.24 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain E Hydrophobic interactions: G:L.16, G:P.24 Water bridges: G:H.23 Hydrogen bonds: E:G.306 MPD.30: 5 residues within 4Å: Chain F: G.306, P.307 Chain H: L.16, H.23, P.24 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain F Hydrophobic interactions: H:L.16, H:P.24 Water bridges: H:H.23 Hydrogen bonds: F:G.306 MPD.35: 5 residues within 4Å: Chain F: L.16, H.23, P.24 Chain G: G.306, P.307 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain G Hydrophobic interactions: F:L.16, F:P.24 Water bridges: F:H.23 Hydrogen bonds: G:G.306 MPD.40: 5 residues within 4Å: Chain E: L.16, H.23, P.24 Chain H: G.306, P.307 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain H Hydrophobic interactions: E:L.16, E:P.24 Water bridges: E:H.23 Hydrogen bonds: H:G.306

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fushinobu, S. et al., Structural basis for the bifunctionality of fructose-1,6-bisphosphate aldolase/phosphatase. Nature (2011)

Release Date

2011-10-12

Peptides

Putative uncharacterized protein ST0318: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

Putative uncharacterized protein ST0318