SMTL ID : 4xz2.1

Human platelet phosphofructokinase in an R-state in complex with ADP and F6P, crystal form I

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.67 Å

Oligo State

homo-tetramer

Ligands

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 6 residues within 4Å: Chain A: G.232, K.263, R.429, R.433, G.466, G.467 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.232, A:G.467 Salt bridges: A:K.263, A:R.429, A:R.433 PO4.6: 6 residues within 4Å: Chain B: G.232, K.263, R.429, R.433, G.466, G.467 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.467 Salt bridges: B:K.263, B:R.429, B:R.433 PO4.7: 9 residues within 4Å: Chain B: R.43, R.47, V.81, S.82, S.83, K.566, G.598, I.629, R.631 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.81, B:S.83 Salt bridges: B:R.43, B:R.47, B:K.566, B:R.631 PO4.9: 6 residues within 4Å: Chain C: G.232, K.263, R.429, R.433, G.466, G.467 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.232, C:G.467 Salt bridges: C:K.263, C:R.429, C:R.433 PO4.13: 6 residues within 4Å: Chain D: G.232, K.263, R.429, R.433, G.466, G.467 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.232, D:G.467 Salt bridges: D:K.263, D:R.429, D:R.433 PO4.14: 9 residues within 4Å: Chain D: R.43, R.47, V.81, S.82, S.83, L.85, K.566, G.598, R.631 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.83 Salt bridges: D:R.43, D:R.47, D:K.566, D:R.631

4 x FBP: 1,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)

FBP.2: 14 residues within 4Å: Chain A: A.419, R.480, T.537, V.538, S.539, N.541, M.582, G.583, G.584, E.638, H.670, Q.673 Chain B: R.575, R.664 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.480, A:S.539, A:S.539, A:G.583, A:G.584, A:E.638, A:E.638, A:Q.673 Salt bridges: A:R.480, A:R.480, A:H.670, B:R.575, B:R.664 FBP.4: 12 residues within 4Å: Chain A: R.575, R.664 Chain B: R.480, T.537, V.538, S.539, N.541, M.582, G.583, E.638, H.670, Q.673 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.480, B:R.480, B:S.539, B:N.541, B:N.541, B:G.583, B:E.638, B:Q.673 Salt bridges: B:R.480, B:R.480, B:H.670, A:R.575, A:R.664 FBP.8: 14 residues within 4Å: Chain C: A.419, R.480, T.537, V.538, S.539, N.541, M.582, G.583, G.584, E.638, H.670, Q.673 Chain D: R.575, R.664 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:R.480, C:S.539, C:N.541, C:G.583, C:G.584, C:E.638, C:E.638, C:Q.673 Salt bridges: C:R.480, C:R.480, C:H.670, D:R.575, D:R.664 FBP.11: 11 residues within 4Å: Chain C: R.664 Chain D: A.419, R.480, T.537, S.539, N.541, M.582, G.583, E.638, H.670, Q.673 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.480, D:T.537, D:S.539, D:G.583, D:G.584, D:E.638, D:E.638, D:Q.673 Salt bridges: D:R.480, D:R.480, D:H.670, C:R.664

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 15 residues within 4Å: Chain B: S.31, G.32, G.33, Y.63, A.95, R.96, C.97, F.100, R.101, G.126, D.127, G.128, S.129, G.132, L.135 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.31, B:S.31, B:G.33, B:R.96, B:R.96, B:C.97, B:C.97, B:R.101, B:G.126, B:D.127, B:G.128, B:S.129 Salt bridges: B:R.96 pi-Cation interactions: B:R.101 ADP.10: 18 residues within 4Å: Chain D: S.31, G.32, G.33, Y.63, A.95, R.96, C.97, F.100, R.101, G.125, G.126, D.127, G.128, S.129, T.131, G.132, L.135, R.218 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:S.31, D:G.33, D:A.95, D:C.97, D:C.97, D:G.126, D:D.127, D:G.128, D:S.129, D:T.131, D:R.218 pi-Cation interactions: D:R.101

2 x F6P: 6-O-phosphono-beta-D-fructofuranose(Non-covalent)

F6P.5: 10 residues within 4Å: Chain A: R.209, R.300 Chain B: I.173, D.174, M.216, G.217, R.218, E.272, H.306, R.309 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.174, B:G.217, B:R.218, B:E.272, B:R.309 Salt bridges: B:H.306, B:R.309, A:R.209, A:R.300 F6P.12: 9 residues within 4Å: Chain C: R.209, R.300 Chain D: I.173, D.174, M.216, R.218, E.272, H.306, R.309 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:D.174, D:R.218, D:E.272, D:R.309 Salt bridges: D:H.306, D:R.309, C:R.209, C:R.300

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kloos, M. et al., Crystal structure of human platelet phosphofructokinase-1 locked in an activated conformation. Biochem.J. (2015)

Release Date

2015-06-03

Peptides

ATP-dependent 6-phosphofructokinase, platelet type: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

ATP-dependent 6-phosphofructokinase, platelet type

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