SMTL ID : 1umg.1

Crystal structure of fructose-1,6-bisphosphatase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-octamer

Ligands

32 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.231, E.345 Ligands: MG.2, 2FP.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.231, H2O.1, H2O.1, H2O.1 MG.2: 6 residues within 4Å: Chain A: D.52, D.231, D.232 Ligands: MG.1, MG.3, 2FP.5 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.231, A:D.232, H2O.1, H2O.1, H2O.1 MG.3: 7 residues within 4Å: Chain A: D.51, D.52, D.130, K.131, D.232 Ligands: MG.2, 2FP.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.51, A:D.52, A:D.130, A:D.232, H2O.1 MG.4: 5 residues within 4Å: Chain A: D.10, H.17, D.51, Q.93 Ligands: 2FP.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.10, A:H.17, A:D.51, H2O.1 MG.7: 4 residues within 4Å: Chain B: D.231, E.345 Ligands: MG.8, 2FP.11 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.231, H2O.11, H2O.11, H2O.11 MG.8: 6 residues within 4Å: Chain B: D.52, D.231, D.232 Ligands: MG.7, MG.9, 2FP.11 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.231, B:D.232, H2O.11, H2O.11, H2O.11 MG.9: 7 residues within 4Å: Chain B: D.51, D.52, D.130, K.131, D.232 Ligands: MG.8, 2FP.11 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.51, B:D.52, B:D.130, B:D.232, H2O.11 MG.10: 5 residues within 4Å: Chain B: D.10, H.17, D.51, Q.93 Ligands: 2FP.11 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.10, B:H.17, B:D.51, H2O.11 MG.13: 4 residues within 4Å: Chain C: D.231, E.345 Ligands: MG.14, 2FP.17 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.231, H2O.21, H2O.21, H2O.21 MG.14: 6 residues within 4Å: Chain C: D.52, D.231, D.232 Ligands: MG.13, MG.15, 2FP.17 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.231, C:D.232, H2O.21, H2O.21, H2O.21 MG.15: 7 residues within 4Å: Chain C: D.51, D.52, D.130, K.131, D.232 Ligands: MG.14, 2FP.17 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.51, C:D.52, C:D.130, C:D.232, H2O.21 MG.16: 5 residues within 4Å: Chain C: D.10, H.17, D.51, Q.93 Ligands: 2FP.17 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.10, C:H.17, C:D.51, H2O.21 MG.19: 4 residues within 4Å: Chain D: D.231, E.345 Ligands: MG.20, 2FP.23 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.231, H2O.31, H2O.31, H2O.31 MG.20: 6 residues within 4Å: Chain D: D.52, D.231, D.232 Ligands: MG.19, MG.21, 2FP.23 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.231, D:D.232, H2O.31, H2O.31, H2O.31 MG.21: 7 residues within 4Å: Chain D: D.51, D.52, D.130, K.131, D.232 Ligands: MG.20, 2FP.23 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.51, D:D.52, D:D.130, D:D.232, H2O.31 MG.22: 5 residues within 4Å: Chain D: D.10, H.17, D.51, Q.93 Ligands: 2FP.23 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.10, D:H.17, D:D.51, H2O.31 MG.25: 4 residues within 4Å: Chain E: D.231, E.345 Ligands: MG.26, 2FP.29 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.231, H2O.41, H2O.41, H2O.41 MG.26: 6 residues within 4Å: Chain E: D.52, D.231, D.232 Ligands: MG.25, MG.27, 2FP.29 5 PLIP interactions: 2 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.231, E:D.232, H2O.41, H2O.41, H2O.41 MG.27: 7 residues within 4Å: Chain E: D.51, D.52, D.130, K.131, D.232 Ligands: MG.26, 2FP.29 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.51, E:D.52, E:D.130, E:D.232, H2O.41 MG.28: 5 residues within 4Å: Chain E: D.10, H.17, D.51, Q.93 Ligands: 2FP.29 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.10, E:H.17, E:D.51, H2O.41 MG.31: 4 residues within 4Å: Chain F: D.231, E.345 Ligands: MG.32, 2FP.35 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.231, H2O.51, H2O.51, H2O.51 MG.32: 6 residues within 4Å: Chain F: D.52, D.231, D.232 Ligands: MG.31, MG.33, 2FP.35 5 PLIP interactions: 2 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.231, F:D.232, H2O.51, H2O.51, H2O.51 MG.33: 7 residues within 4Å: Chain F: D.51, D.52, D.130, K.131, D.232 Ligands: MG.32, 2FP.35 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.51, F:D.52, F:D.130, F:D.232, H2O.51 MG.34: 5 residues within 4Å: Chain F: D.10, H.17, D.51, Q.93 Ligands: 2FP.35 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.10, F:H.17, F:D.51, H2O.51 MG.37: 4 residues within 4Å: Chain G: D.231, E.345 Ligands: MG.38, 2FP.41 4 PLIP interactions: 1 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:D.231, H2O.61, H2O.61, H2O.61 MG.38: 6 residues within 4Å: Chain G: D.52, D.231, D.232 Ligands: MG.37, MG.39, 2FP.41 5 PLIP interactions: 2 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:D.231, G:D.232, H2O.61, H2O.61, H2O.61 MG.39: 7 residues within 4Å: Chain G: D.51, D.52, D.130, K.131, D.232 Ligands: MG.38, 2FP.41 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.51, G:D.52, G:D.130, G:D.232, H2O.61 MG.40: 5 residues within 4Å: Chain G: D.10, H.17, D.51, Q.93 Ligands: 2FP.41 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.10, G:H.17, G:D.51, H2O.61 MG.43: 4 residues within 4Å: Chain H: D.231, E.345 Ligands: MG.44, 2FP.47 4 PLIP interactions: 1 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:D.231, H2O.71, H2O.71, H2O.71 MG.44: 6 residues within 4Å: Chain H: D.52, D.231, D.232 Ligands: MG.43, MG.45, 2FP.47 5 PLIP interactions: 2 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:D.231, H:D.232, H2O.71, H2O.71, H2O.71 MG.45: 7 residues within 4Å: Chain H: D.51, D.52, D.130, K.131, D.232 Ligands: MG.44, 2FP.47 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.51, H:D.52, H:D.130, H:D.232, H2O.71 MG.46: 5 residues within 4Å: Chain H: D.10, H.17, D.51, Q.93 Ligands: 2FP.47 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.10, H:H.17, H:D.51, H2O.71

8 x 2FP: 1,6-FRUCTOSE DIPHOSPHATE (LINEAR FORM)(Non-covalent)

2FP.5: 25 residues within 4Å: Chain A: D.10, H.17, D.51, Y.89, Q.93, S.101, G.102, N.103, D.130, K.131, D.231, D.232, W.262, M.263, R.264, G.265, D.285, Y.346 Chain D: Q.240, H.241, A.245 Ligands: MG.1, MG.2, MG.3, MG.4 24 PLIP interactions: 17 interactions with chain A, 7 interactions with chain D Hydrogen bonds: A:Y.89, A:Y.89, A:Q.93, A:G.102, A:N.103, A:R.264, A:G.265, A:D.285, A:Y.346, A:Y.346, D:Q.240, D:Q.240, D:Q.240, D:H.241 Water bridges: A:H.17, A:K.131, A:D.231, A:R.264, D:G.242, D:G.242, D:L.243 Salt bridges: A:H.17, A:H.17, A:K.131 2FP.11: 25 residues within 4Å: Chain B: D.10, H.17, D.51, Y.89, Q.93, S.101, G.102, N.103, D.130, K.131, D.231, D.232, W.262, M.263, R.264, G.265, D.285, Y.346 Chain C: Q.240, H.241, A.245 Ligands: MG.7, MG.8, MG.9, MG.10 24 PLIP interactions: 7 interactions with chain C, 17 interactions with chain B Hydrogen bonds: C:Q.240, C:Q.240, C:Q.240, C:H.241, B:Y.89, B:Y.89, B:Q.93, B:G.102, B:N.103, B:R.264, B:G.265, B:D.285, B:Y.346, B:Y.346 Water bridges: C:G.242, C:G.242, C:L.243, B:H.17, B:K.131, B:D.231, B:R.264 Salt bridges: B:H.17, B:H.17, B:K.131 2FP.17: 25 residues within 4Å: Chain A: Q.240, H.241, A.245 Chain C: D.10, H.17, D.51, Y.89, Q.93, S.101, G.102, N.103, D.130, K.131, D.231, D.232, W.262, M.263, R.264, G.265, D.285, Y.346 Ligands: MG.13, MG.14, MG.15, MG.16 26 PLIP interactions: 7 interactions with chain A, 19 interactions with chain C Hydrogen bonds: A:Q.240, A:Q.240, A:Q.240, A:H.241, C:Y.89, C:Y.89, C:Q.93, C:G.102, C:N.103, C:R.264, C:G.265, C:D.285, C:Y.346, C:Y.346 Water bridges: A:G.242, A:G.242, A:L.243, C:H.17, C:K.131, C:D.231, C:D.232, C:D.232, C:R.264 Salt bridges: C:H.17, C:H.17, C:K.131 2FP.23: 25 residues within 4Å: Chain B: Q.240, H.241, A.245 Chain D: D.10, H.17, D.51, Y.89, Q.93, S.101, G.102, N.103, D.130, K.131, D.231, D.232, W.262, M.263, R.264, G.265, D.285, Y.346 Ligands: MG.19, MG.20, MG.21, MG.22 24 PLIP interactions: 17 interactions with chain D, 7 interactions with chain B Hydrogen bonds: D:Y.89, D:Y.89, D:Q.93, D:G.102, D:N.103, D:R.264, D:G.265, D:D.285, D:Y.346, D:Y.346, B:Q.240, B:Q.240, B:Q.240, B:H.241 Water bridges: D:H.17, D:K.131, D:D.231, D:R.264, B:G.242, B:G.242, B:L.243 Salt bridges: D:H.17, D:H.17, D:K.131 2FP.29: 25 residues within 4Å: Chain E: D.10, H.17, D.51, Y.89, Q.93, S.101, G.102, N.103, D.130, K.131, D.231, D.232, W.262, M.263, R.264, G.265, D.285, Y.346 Chain H: Q.240, H.241, A.245 Ligands: MG.25, MG.26, MG.27, MG.28 26 PLIP interactions: 19 interactions with chain E, 7 interactions with chain H Hydrogen bonds: E:D.10, E:Y.89, E:Q.93, E:G.102, E:N.103, E:R.264, E:G.265, E:D.285, E:D.285, E:Y.346, E:Y.346, H:Q.240, H:Q.240, H:Q.240, H:H.241 Water bridges: E:H.17, E:D.51, E:K.131, E:D.231, E:R.264, H:G.242, H:G.242, H:L.243 Salt bridges: E:H.17, E:H.17, E:K.131 2FP.35: 25 residues within 4Å: Chain F: D.10, H.17, D.51, Y.89, Q.93, S.101, G.102, N.103, D.130, K.131, D.231, D.232, W.262, M.263, R.264, G.265, D.285, Y.346 Chain G: Q.240, H.241, A.245 Ligands: MG.31, MG.32, MG.33, MG.34 26 PLIP interactions: 19 interactions with chain F, 7 interactions with chain G Hydrogen bonds: F:D.10, F:Y.89, F:Q.93, F:G.102, F:N.103, F:R.264, F:G.265, F:D.285, F:D.285, F:Y.346, F:Y.346, G:Q.240, G:Q.240, G:Q.240, G:H.241 Water bridges: F:H.17, F:D.51, F:K.131, F:D.231, F:R.264, G:G.242, G:G.242, G:L.243 Salt bridges: F:H.17, F:H.17, F:K.131 2FP.41: 25 residues within 4Å: Chain E: Q.240, H.241, A.245 Chain G: D.10, H.17, D.51, Y.89, Q.93, S.101, G.102, N.103, D.130, K.131, D.231, D.232, W.262, M.263, R.264, G.265, D.285, Y.346 Ligands: MG.37, MG.38, MG.39, MG.40 26 PLIP interactions: 19 interactions with chain G, 7 interactions with chain E Hydrogen bonds: G:D.10, G:Y.89, G:Q.93, G:G.102, G:N.103, G:R.264, G:G.265, G:D.285, G:D.285, G:Y.346, G:Y.346, E:Q.240, E:Q.240, E:Q.240, E:H.241 Water bridges: G:H.17, G:D.51, G:K.131, G:D.231, G:R.264, E:G.242, E:G.242, E:L.243 Salt bridges: G:H.17, G:H.17, G:K.131 2FP.47: 25 residues within 4Å: Chain F: Q.240, H.241, A.245 Chain H: D.10, H.17, D.51, Y.89, Q.93, S.101, G.102, N.103, D.130, K.131, D.231, D.232, W.262, M.263, R.264, G.265, D.285, Y.346 Ligands: MG.43, MG.44, MG.45, MG.46 27 PLIP interactions: 20 interactions with chain H, 7 interactions with chain F Hydrogen bonds: H:D.10, H:Y.89, H:Q.93, H:G.102, H:N.103, H:R.264, H:G.265, H:D.285, H:D.285, H:Y.346, H:Y.346, F:Q.240, F:Q.240, F:Q.240, F:H.241 Water bridges: H:H.17, H:D.51, H:K.131, H:D.231, H:D.231, H:R.264, F:G.242, F:G.242, F:L.243 Salt bridges: H:H.17, H:H.17, H:K.131

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

MPD.6: 5 residues within 4Å: Chain A: D.315 Chain C: D.315, R.318, R.319, N.322 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Water bridges: A:E.316, A:E.316 Hydrophobic interactions: C:R.318, C:R.319 MPD.12: 5 residues within 4Å: Chain B: D.315 Chain D: D.315, R.318, R.319, N.322 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:R.318, D:R.319 Water bridges: B:E.316, B:E.316 MPD.18: 5 residues within 4Å: Chain B: D.315, R.318, R.319, N.322 Chain C: D.315 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:R.318, B:R.319 Water bridges: C:E.316, C:E.316 MPD.24: 5 residues within 4Å: Chain A: D.315, R.318, R.319, N.322 Chain D: D.315 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Water bridges: D:E.316, D:E.316 Hydrophobic interactions: A:R.318, A:R.319 MPD.30: 5 residues within 4Å: Chain E: D.315 Chain G: D.315, R.318, R.319, N.322 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain G Hydrogen bonds: E:D.315 Water bridges: E:E.316 Hydrophobic interactions: G:R.318, G:R.319 MPD.36: 5 residues within 4Å: Chain F: D.315 Chain H: D.315, R.318, R.319, N.322 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain H Hydrogen bonds: F:D.315 Water bridges: F:E.316 Hydrophobic interactions: H:R.318, H:R.319 MPD.42: 5 residues within 4Å: Chain F: D.315, R.318, R.319, N.322 Chain G: D.315 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain G Hydrophobic interactions: F:R.318, F:R.319 Hydrogen bonds: G:D.315 Water bridges: G:E.316 MPD.48: 5 residues within 4Å: Chain E: D.315, R.318, R.319, N.322 Chain H: D.315 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain H Hydrophobic interactions: E:R.318, E:R.319 Hydrogen bonds: H:D.315 Water bridges: H:E.316

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nishimasu, H. et al., The first crystal structure of the novel class of fructose-1,6-bisphosphatase present in thermophilic archaea. Structure (2004)

Release Date

2004-07-13

Peptides

385aa long conserved hypothetical protein: 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

385aa long conserved hypothetical protein