SMTL ID : 3opy.1

Crystal structure of Pichia pastoris phosphofructokinase in the T-state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.05 Å

Oligo State

hetero-4-4-4-mer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: G.219, G.220, G.313, D.314, G.315, S.316 Ligands: SO4.2 Ligand excluded by PLIP SO4.2: 8 residues within 4Å: Chain A: G.220, D.314, G.358, S.359, I.360, D.361, R.496 Ligands: SO4.1 Ligand excluded by PLIP SO4.3: 4 residues within 4Å: Chain A: R.635, N.636 Chain B: K.797 Ligands: SO4.4 Ligand excluded by PLIP SO4.4: 6 residues within 4Å: Chain A: R.635, N.636 Chain B: Q.793, G.794, K.797 Ligands: SO4.3 Ligand excluded by PLIP SO4.5: 5 residues within 4Å: Chain A: A.608, R.670, H.864 Chain B: R.739, K.832 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: T.575, R.881, K.885 Ligand excluded by PLIP SO4.7: 8 residues within 4Å: Chain A: R.230, R.234, V.268, R.269, G.270, L.272, K.756, G.788 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain A: R.324, P.524, P.527, S.528 Ligand excluded by PLIP SO4.9: 5 residues within 4Å: Chain A: R.670, S.729, N.731, G.774, K.961 Ligand excluded by PLIP SO4.10: 5 residues within 4Å: Chain A: R.396, R.487 Chain B: M.375, H.466, R.469 Ligand excluded by PLIP SO4.11: 5 residues within 4Å: Chain A: E.401, T.471, S.472, E.473, R.490 Ligand excluded by PLIP SO4.12: 7 residues within 4Å: Chain A: R.451, R.618, V.655, E.656, D.657, W.658, H.659 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain A: S.857, R.858, T.859 Ligand excluded by PLIP SO4.15: 5 residues within 4Å: Chain A: M.403, H.493, R.496 Chain B: R.368, R.460 Ligand excluded by PLIP SO4.16: 9 residues within 4Å: Chain B: R.201, R.205, V.240, R.241, G.242, K.730, G.762, S.798 Chain I: D.351 Ligand excluded by PLIP SO4.17: 8 residues within 4Å: Chain C: R.230, R.234, V.268, R.269, G.270, L.272, K.756, G.788 Ligand excluded by PLIP SO4.18: 7 residues within 4Å: Chain C: G.220, G.358, S.359, I.360, D.361, R.496 Ligands: SO4.19 Ligand excluded by PLIP SO4.19: 7 residues within 4Å: Chain C: G.219, G.220, G.313, D.314, G.315, S.316 Ligands: SO4.18 Ligand excluded by PLIP SO4.20: 5 residues within 4Å: Chain C: A.608, R.670, H.864 Chain D: R.739, K.832 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain C: R.635 Chain D: K.797 Ligands: SO4.29 Ligand excluded by PLIP SO4.22: 5 residues within 4Å: Chain C: R.324, P.524, I.526, P.527, S.528 Ligand excluded by PLIP SO4.23: 6 residues within 4Å: Chain C: R.396, D.485, R.487 Chain D: M.375, H.466, R.469 Ligand excluded by PLIP SO4.24: 5 residues within 4Å: Chain C: E.401, T.471, S.472, E.473, R.490 Ligand excluded by PLIP SO4.25: 7 residues within 4Å: Chain C: R.451, R.618, V.655, E.656, D.657, W.658, H.659 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain C: R.858, T.859 Chain D: H.838 Ligand excluded by PLIP SO4.28: 8 residues within 4Å: Chain D: R.201, R.205, R.241, G.242, K.730, G.762, S.798 Chain J: D.351 Ligand excluded by PLIP SO4.29: 5 residues within 4Å: Chain C: R.635 Chain D: Q.793, G.794, K.797 Ligands: SO4.21 Ligand excluded by PLIP SO4.30: 5 residues within 4Å: Chain C: M.403, H.493, R.496 Chain D: R.368, R.460 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain A: G.917 Chain E: R.643, H.644 Chain F: R.828 Ligand excluded by PLIP SO4.32: 5 residues within 4Å: Chain E: A.608, R.670, H.864 Chain F: R.739, K.832 Ligand excluded by PLIP SO4.33: 6 residues within 4Å: Chain E: G.220, D.314, S.359, I.360, D.361, R.496 Ligand excluded by PLIP SO4.34: 8 residues within 4Å: Chain E: R.230, R.234, V.268, R.269, G.270, L.272, K.756, G.788 Ligand excluded by PLIP SO4.35: 4 residues within 4Å: Chain E: R.324, P.524, P.527, S.528 Ligand excluded by PLIP SO4.36: 5 residues within 4Å: Chain E: R.396, R.487 Chain F: M.375, H.466, R.469 Ligand excluded by PLIP SO4.37: 5 residues within 4Å: Chain E: E.401, T.471, S.472, E.473, R.490 Ligand excluded by PLIP SO4.38: 7 residues within 4Å: Chain E: R.451, R.618, V.655, E.656, D.657, W.658, H.659 Ligand excluded by PLIP SO4.40: 9 residues within 4Å: Chain F: R.201, R.205, V.240, R.241, G.242, L.244, K.730, G.762, S.798 Ligand excluded by PLIP SO4.41: 5 residues within 4Å: Chain E: M.403, H.493, R.496 Chain F: R.368, R.460 Ligand excluded by PLIP SO4.42: 5 residues within 4Å: Chain E: R.635 Chain F: D.792, Q.793, G.794, K.797 Ligand excluded by PLIP SO4.43: 8 residues within 4Å: Chain G: G.220, D.314, G.358, S.359, I.360, D.361, R.496 Ligands: SO4.45 Ligand excluded by PLIP SO4.44: 7 residues within 4Å: Chain G: R.230, R.234, V.268, R.269, G.270, K.756, G.788 Ligand excluded by PLIP SO4.45: 9 residues within 4Å: Chain G: S.218, G.219, G.220, G.312, G.313, D.314, G.315, S.316 Ligands: SO4.43 Ligand excluded by PLIP SO4.46: 6 residues within 4Å: Chain G: R.670, T.727, S.729, N.731, G.774, K.961 Ligand excluded by PLIP SO4.47: 5 residues within 4Å: Chain G: A.608, R.670, H.864 Chain H: R.739, K.832 Ligand excluded by PLIP SO4.48: 6 residues within 4Å: Chain G: R.396, D.485, R.487 Chain H: M.375, H.466, R.469 Ligand excluded by PLIP SO4.49: 5 residues within 4Å: Chain G: E.401, T.471, S.472, E.473, R.490 Ligand excluded by PLIP SO4.50: 6 residues within 4Å: Chain G: R.451, R.618, V.655, E.656, D.657, H.659 Ligand excluded by PLIP SO4.52: 8 residues within 4Å: Chain H: R.201, R.205, R.241, G.242, K.730, G.762, S.798 Chain L: D.351 Ligand excluded by PLIP SO4.53: 4 residues within 4Å: Chain G: R.635 Chain H: Q.793, G.794, K.797 Ligand excluded by PLIP SO4.54: 5 residues within 4Å: Chain G: M.403, H.493, R.496 Chain H: R.368, R.460 Ligand excluded by PLIP SO4.55: 5 residues within 4Å: Chain C: G.917 Chain G: R.643, H.644 Chain H: N.738, R.828 Ligand excluded by PLIP SO4.56: 3 residues within 4Å: Chain I: R.93, D.250, T.251 Ligand excluded by PLIP SO4.57: 5 residues within 4Å: Chain I: N.128, S.129, K.200, R.204, M.218 Ligand excluded by PLIP SO4.58: 3 residues within 4Å: Chain I: D.5, S.6, R.9 Ligand excluded by PLIP SO4.59: 2 residues within 4Å: Chain I: N.76, N.77 Ligand excluded by PLIP SO4.60: 3 residues within 4Å: Chain I: G.180, P.181, H.196 Ligand excluded by PLIP SO4.61: 5 residues within 4Å: Chain J: G.180, P.181, H.196, L.198, Y.230 Ligand excluded by PLIP SO4.62: 3 residues within 4Å: Chain J: S.129, K.200, R.204 Ligand excluded by PLIP SO4.63: 3 residues within 4Å: Chain J: D.5, S.6, R.9 Ligand excluded by PLIP SO4.64: 5 residues within 4Å: Chain K: R.93, N.248, F.249, D.250, T.251 Ligand excluded by PLIP SO4.65: 3 residues within 4Å: Chain K: S.129, K.200, R.204 Ligand excluded by PLIP SO4.66: 2 residues within 4Å: Chain K: N.76, N.77 Ligand excluded by PLIP SO4.67: 3 residues within 4Å: Chain L: D.5, S.6, R.9 Ligand excluded by PLIP SO4.68: 3 residues within 4Å: Chain L: N.76, N.77, Y.78 Ligand excluded by PLIP SO4.69: 5 residues within 4Å: Chain L: G.180, P.181, H.196, L.198, Y.230 Ligand excluded by PLIP

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.14: 14 residues within 4Å: Chain B: D.393, Y.394, I.395, K.400, A.402, S.403, S.404, R.405, Q.410, I.414, F.553, I.554, N.557, S.558 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:I.395, B:I.395, B:P.401, B:S.403, B:S.404, B:R.405, B:Q.410, B:N.557 Salt bridges: B:K.400, B:K.400, B:R.405 ATP.27: 14 residues within 4Å: Chain D: D.393, Y.394, I.395, K.400, A.402, S.403, S.404, R.405, Q.410, I.414, F.553, I.554, N.557, S.558 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:I.395, D:I.395, D:P.401, D:S.403, D:S.404, D:Q.410, D:N.557, D:N.557 Salt bridges: D:K.400, D:K.400, D:R.405 ATP.39: 15 residues within 4Å: Chain F: D.393, Y.394, I.395, K.400, P.401, A.402, S.403, S.404, R.405, Q.410, I.414, F.553, I.554, N.557, S.558 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:I.395, F:I.395, F:S.403, F:S.404, F:Q.410, F:N.557, F:N.557 Salt bridges: F:K.400, F:K.400, F:R.405 ATP.51: 15 residues within 4Å: Chain H: D.393, Y.394, I.395, K.400, P.401, A.402, S.403, S.404, R.405, Q.410, I.414, F.553, I.554, N.557, S.558 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:I.395, H:I.395, H:S.403, H:S.404, H:Q.410, H:N.557, H:N.557 Salt bridges: H:K.400, H:K.400, H:R.405

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Strater, N. et al., Molecular architecture and structural basis of allosteric regulation of eukaryotic phosphofructokinases. Faseb J. (2011)

Release Date

2010-10-06

Peptides

6-phosphofructo-1-kinase alpha-subunit: ACEG
6-phosphofructo-1-kinase beta-subunit: BDFH
6-phosphofructo-1-kinase gamma-subunit: IJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

B
B

D
D

F
F

H
H

I
I

J
J

K
K

L
L

6-phosphofructo-1-kinase alpha-subunit

6-phosphofructo-1-kinase beta-subunit

6-phosphofructo-1-kinase gamma-subunit