SMTL ID : 4foi.1 (2 other biounits)

Crystal Structure of recombinant human Hexokinase type I mutant D413N with Glucose 1,6-bisphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

4 x BGC: beta-D-glucopyranose(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:N.235, A:E.260, A:E.260, A:Q.291 Water bridges: A:G.233, A:G.233 Salt bridges: A:K.173 BGC.3: 14 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, N.683, E.708, Q.739, E.742 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.603, A:K.621, A:N.656, A:N.656, A:N.683, A:E.708, A:E.708, A:Q.739 Water bridges: A:G.681, A:G.681, A:E.708, A:E.708 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 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.603, B:K.621, B:N.656, B:N.656, B:D.657, B:N.683, B:E.708, B:E.708, B:Q.739 Salt bridges: B:K.621

4 x G16: 1,6-di-O-phosphono-alpha-D-glucopyranose(Non-covalent)

G16.2: 15 residues within 4Å: Chain A: D.84, G.87, S.88, S.89, R.91, T.153, D.209, I.229, G.231, T.232, N.413, G.414, S.415, K.418, S.449 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:D.84, A:S.88, A:R.91, A:D.209, A:D.209, A:T.232, A:T.232, A:G.414, A:S.415, A:S.449, A:S.449 Water bridges: A:G.233 Salt bridges: A:R.91, A:K.418 G16.4: 15 residues within 4Å: Chain A: D.532, G.535, T.536, N.537, R.539, S.603, D.657, I.677, G.679, T.680, D.861, G.862, T.863, G.896, S.897 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:D.532, A:T.536, A:T.536, A:N.537, A:N.537, 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:R.539, A:R.539, A:D.861, A:G.862, A:G.898 Salt bridges: A:R.539 G16.9: 15 residues within 4Å: Chain B: D.84, G.87, S.88, S.89, R.91, D.209, I.229, G.231, T.232, N.413, G.414, S.415, K.418, G.448, S.449 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:D.84, B:S.88, B:T.232, B:T.232, B:S.415, B:S.449, B:S.449 Water bridges: B:D.84, B:G.87, B:G.231, B:G.233, B:G.414, B:L.416, B:K.418 Salt bridges: B:R.91, B:K.418, B:K.418 G16.11: 14 residues within 4Å: Chain B: D.532, G.535, T.536, N.537, R.539, D.657, I.677, G.679, T.680, D.861, G.862, T.863, G.896, S.897 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:D.532, B:T.536, B:N.537, B:T.680, B:T.680, B:T.863, B:S.897, B:S.897 Water bridges: B:G.681 Salt bridges: B:R.539

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

NA.5: 4 residues within 4Å: Chain A: L.242, I.245, V.248, G.250 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.250, A:G.250 NA.6: 4 residues within 4Å: Chain A: M.690, V.693, 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, I.245, V.248, E.249, G.250 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.248 NA.13: 5 residues within 4Å: Chain B: M.690, V.693, E.694, V.696, G.698 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.690

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

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, L. et al., DETERMINATION of SITE AFFINITY CONSTANTS FOR PRODUCT INHIBITION OF WILD-TYPE AND 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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