SMTL ID : 2nzt.1

Crystal structure of human hexokinase II

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

4 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.1: 16 residues within 4Å: Chain A: S.141, F.142, P.143, T.158, K.159, N.194, D.195, T.196, I.215, G.219, S.220, N.221, E.246, Q.277, E.280 Ligands: UNX.13 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.158, A:K.159, A:N.194, A:N.194, A:D.195, A:N.221, A:E.246, A:Q.277 Water bridges: A:G.219 Salt bridges: A:K.159 GLC.3: 15 residues within 4Å: Chain A: S.589, F.590, P.591, T.606, K.607, N.642, D.643, T.644, I.663, G.667, S.668, N.669, E.694, Q.725, E.728 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:T.606, A:T.606, A:K.607, A:N.642, A:N.642, A:S.668, A:N.669, A:E.694, A:Q.725, A:E.728 Water bridges: A:K.607, A:G.667 Salt bridges: A:K.607 GLC.17: 14 residues within 4Å: Chain B: S.141, F.142, P.143, T.158, K.159, N.194, D.195, I.215, G.219, S.220, N.221, E.246, Q.277, E.280 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:T.158, B:K.159, B:N.194, B:N.194, B:S.220, B:N.221, B:E.246, B:Q.277 Water bridges: B:S.220, B:E.246 Salt bridges: B:K.159 GLC.19: 15 residues within 4Å: Chain B: S.589, F.590, P.591, T.606, K.607, N.642, D.643, T.644, I.663, G.667, S.668, N.669, E.694, Q.725, E.728 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:T.606, B:T.606, B:K.607, B:N.642, B:N.642, B:S.668, B:N.669, B:E.694, B:Q.725 Water bridges: B:S.668, B:E.694 Salt bridges: B:K.607

4 x BG6: 6-O-phosphono-beta-D-glucopyranose(Non-covalent)

BG6.2: 14 residues within 4Å: Chain A: D.70, G.73, T.74, T.139, S.141, D.195, I.215, G.217, T.218, D.399, G.400, S.401, G.434, S.435 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.70, A:T.74, A:S.141, A:S.141, A:T.218, A:G.400, A:S.401, A:S.435, A:S.435 Water bridges: A:K.159, A:G.219 BG6.4: 14 residues within 4Å: Chain A: D.518, G.521, T.522, T.587, S.589, D.643, I.663, G.665, T.666, D.847, G.848, T.849, G.882, S.883 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.518, A:T.522, A:S.589, A:S.589, A:D.643, A:T.666, A:T.666, A:T.849, A:S.883, A:S.883 Water bridges: A:G.521 BG6.18: 14 residues within 4Å: Chain B: D.70, G.73, T.74, T.139, S.141, D.195, I.215, G.217, T.218, D.399, G.400, S.401, G.434, S.435 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:D.70, B:T.74, B:S.141, B:S.141, B:D.195, B:T.218, B:G.400, B:S.401, B:S.435, B:S.435 BG6.20: 13 residues within 4Å: Chain B: D.518, G.521, T.522, T.587, S.589, D.643, G.665, T.666, D.847, G.848, T.849, G.882, S.883 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:D.518, B:T.522, B:S.589, B:S.589, B:D.643, B:T.666, B:T.666, B:D.847, B:T.849, B:S.883, B:S.883 Water bridges: B:G.521, B:G.882

28 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.5: 7 residues within 4Å: Chain A: E.32, K.35, T.44, A.45, A.46, D.253 Ligands: UNX.6 Ligand excluded by PLIP UNX.6: 6 residues within 4Å: Chain A: E.32, K.35, A.45, A.46, V.47 Ligands: UNX.5 Ligand excluded by PLIP UNX.7: 4 residues within 4Å: Chain A: D.70, G.72, G.73, N.75 Ligand excluded by PLIP UNX.8: 4 residues within 4Å: Chain A: F.140, F.142, C.144, N.194 Ligand excluded by PLIP UNX.9: 4 residues within 4Å: Chain A: P.407, H.408, A.410, K.411 Ligand excluded by PLIP UNX.10: 1 residues within 4Å: Chain A: R.456 Ligand excluded by PLIP UNX.11: 4 residues within 4Å: Chain A: M.228, I.231, G.236 Ligands: UNX.16 Ligand excluded by PLIP UNX.12: 2 residues within 4Å: Chain A: T.709, E.710 Ligand excluded by PLIP UNX.13: 7 residues within 4Å: Chain A: S.220, N.221, E.246, W.247, G.248, Q.277 Ligands: GLC.1 Ligand excluded by PLIP UNX.14: 3 residues within 4Å: Chain A: H.63, A.444, Y.447 Ligand excluded by PLIP UNX.15: 2 residues within 4Å: Chain A: R.475, R.476 Ligand excluded by PLIP UNX.16: 5 residues within 4Å: Chain A: M.228, I.231, V.234, G.236 Ligands: UNX.11 Ligand excluded by PLIP UNX.21: 6 residues within 4Å: Chain B: I.104, G.107, S.108, Q.111, L.112, S.163 Ligand excluded by PLIP UNX.22: 4 residues within 4Å: Chain B: L.50, F.142, C.144, N.244 Ligand excluded by PLIP UNX.23: 4 residues within 4Å: Chain B: M.676, V.679, V.682, G.684 Ligand excluded by PLIP UNX.24: 2 residues within 4Å: Chain B: P.312, E.313 Ligand excluded by PLIP UNX.25: 5 residues within 4Å: Chain B: M.228, R.229, I.231, G.236 Ligands: UNX.36 Ligand excluded by PLIP UNX.26: 5 residues within 4Å: Chain B: L.850, Y.851, H.854, F.857, A.858 Ligand excluded by PLIP UNX.27: 5 residues within 4Å: Chain B: L.773, E.777, C.809, A.813, H.854 Ligand excluded by PLIP UNX.28: 5 residues within 4Å: Chain B: N.523, F.524, Y.546, A.547, I.548 Ligand excluded by PLIP UNX.29: 5 residues within 4Å: Chain B: T.647, D.847, S.879, G.882, S.883 Ligand excluded by PLIP UNX.30: 2 residues within 4Å: Chain B: R.448, L.449 Ligand excluded by PLIP UNX.31: 2 residues within 4Å: Chain B: H.453, R.456 Ligand excluded by PLIP UNX.32: 6 residues within 4Å: Chain B: E.480, R.483, G.484, A.493, P.494, V.495 Ligand excluded by PLIP UNX.33: 2 residues within 4Å: Chain B: T.709, E.710 Ligand excluded by PLIP UNX.34: 2 residues within 4Å: Chain B: R.418, F.428 Ligand excluded by PLIP UNX.35: 6 residues within 4Å: Chain B: G.236, D.237, E.238, R.787, T.798, C.799 Ligand excluded by PLIP UNX.36: 5 residues within 4Å: Chain B: M.228, I.231, V.234, G.236 Ligands: UNX.25 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nawaz, M.H. et al., The catalytic inactivation of the N-half of human hexokinase 2 and structural and biochemical characterization of its mitochondrial conformation. Biosci.Rep. (2018)

Release Date

2006-12-05

Peptides

Hexokinase-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hexokinase-2