SMTL ID : 4foe.1

Crystal Structure of recombinant human Hexokinase type I with Mannose 6-Phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

4 x BGC: beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

BGC.1: 14 residues within 4Å: Chain A: S.155, F.156, P.157, T.172, K.173, N.208, D.209, T.210, I.229, G.233, N.235, E.260, Q.291, E.294 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:T.172, A:K.173, A:N.208, A:N.208, A:D.209, A:N.235, A:E.260, A:E.260, A:Q.291, A:E.294 Salt bridges: A:K.173 BGC.3: 15 residues within 4Å: Chain A: S.603, F.604, P.605, T.620, K.621, N.656, D.657, T.658, I.677, G.681, S.682, N.683, E.708, Q.739, E.742 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.603, A:S.603, A:K.621, A:N.656, A:N.656, A:N.683, A:E.708 Water bridges: A:G.681, A:G.681 Salt bridges: A:K.621 BGC.8: 15 residues within 4Å: Chain B: S.155, F.156, P.157, T.172, K.173, N.208, D.209, T.210, I.229, G.233, T.234, N.235, E.260, Q.291, E.294 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.155, B:K.173, B:N.208, B:N.208, B:D.209, B:N.235, B:E.260, B:E.260, B:Q.291 Salt bridges: B:K.173 BGC.10: 15 residues within 4Å: Chain B: S.603, F.604, P.605, T.620, K.621, N.656, D.657, T.658, I.677, G.681, S.682, N.683, E.708, Q.739, E.742 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:S.603, B:K.621, B:N.656, B:N.656, B:N.683, B:E.708, B:E.708, B:Q.739 Water bridges: B:K.621, B:S.682, B:E.708 Salt bridges: B:K.621

4 x M6D: 6-O-phosphono-beta-D-mannopyranose(Non-covalent)

M6D.2: 14 residues within 4Å: Chain A: D.84, G.87, S.88, T.153, S.155, D.209, I.229, G.231, T.232, D.413, G.414, S.415, G.448, S.449 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:D.84, A:S.88, A:S.155, A:S.155, A:D.209, A:T.232, A:T.232, A:G.414, A:S.415, A:S.415, A:S.415, A:G.448, A:S.449 Water bridges: A:K.418 Salt bridges: A:K.418 M6D.4: 14 residues within 4Å: Chain A: D.532, G.535, T.536, T.601, S.603, D.657, I.677, G.679, T.680, D.861, G.862, T.863, G.896, S.897 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:D.532, A:T.536, A:S.603, A:S.603, A:T.680, A:D.861, A:T.863, A:S.897, A:S.897 Water bridges: A:G.535, A:G.535, A:T.680, A:G.681, A:L.864 M6D.9: 13 residues within 4Å: Chain B: D.84, G.87, S.88, T.153, D.209, I.229, G.231, T.232, D.413, G.414, S.415, G.448, S.449 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:D.84, B:S.88, B:S.88, B:T.232, B:T.232, B:D.413, B:D.413, B:S.415, B:S.449, B:S.449 Water bridges: B:D.84, B:G.87, B:T.232, B:G.233, B:K.418 M6D.11: 11 residues within 4Å: Chain B: D.532, G.535, T.536, D.657, G.679, T.680, D.861, G.862, T.863, G.896, S.897 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:D.532, B:T.536, B:T.680, B:T.680, B:D.861, B:T.863, B:S.897 Water bridges: B:G.535, B:S.603, B:G.681 Salt bridges: B:K.866

4 x NA: SODIUM ION(Non-functional Binders)

NA.5: 4 residues within 4Å: Chain A: L.242, I.245, V.248, G.250 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.245, A:G.250, A:G.250 NA.6: 5 residues within 4Å: Chain A: M.690, V.693, E.694, V.696, G.698 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.698 NA.12: 5 residues within 4Å: Chain B: L.242, R.243, I.245, V.248, G.250 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.248 NA.13: 4 residues within 4Å: Chain B: M.690, V.693, V.696, G.698 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.696

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.7: 4 residues within 4Å: Chain A: F.380, R.425, R.426, K.429 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.380 Salt bridges: A:R.425, A:R.425, A:R.426, A:K.429, A:K.429 CIT.14: 4 residues within 4Å: Chain B: F.380, Q.422, R.425, R.426 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.380 Hydrogen bonds: B:N.345 Salt bridges: B:R.425, B:R.425, B:R.426

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, L. et al., Inhibitor Sites of Unequal Affinity Linked by Binding Synergism in Mutant Forms of Recombinant Human Hexokinase Type-I. to be published

Release Date

2013-07-03

Peptides

Hexokinase-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hexokinase-1

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