SMTL ID : 6ude.1

Crystal structure of Glycerol kinase from Elizabethkingia anophelis NUHP1 in complex with ADP and glycerol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

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

ADP.1: 14 residues within 4Å: Chain A: R.26, G.274, T.275, G.318, A.319, I.321, Q.322, S.334, S.335, G.418, G.419, A.420, A.422 Ligands: MG.3 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:G.274, A:T.275, A:T.275, A:Q.322, A:S.334, A:G.419 Water bridges: A:D.19, A:T.22, A:T.22, A:R.26, A:R.26, A:R.26, A:R.26, A:Q.41, A:G.276, A:S.334, A:S.335, A:T.447 Salt bridges: A:R.26, A:R.26 ADP.4: 13 residues within 4Å: Chain B: R.26, G.274, T.275, G.318, A.319, I.321, Q.322, S.334, S.335, G.418, G.419, A.420 Ligands: MG.6 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:G.274, B:T.275, B:T.275, B:Q.322, B:S.334, B:G.419 Water bridges: B:D.19, B:T.22, B:R.26, B:Q.41, B:Q.254, B:T.275, B:S.334, B:S.334, B:S.335, B:A.422 Salt bridges: B:R.26, B:R.26 ADP.7: 15 residues within 4Å: Chain C: T.22, R.26, G.274, T.275, G.318, A.319, I.321, Q.322, S.334, S.335, G.418, G.419, A.420, S.423 Ligands: MG.9 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:T.22, C:G.274, C:T.275, C:Q.322, C:S.334, C:G.419 Water bridges: C:S.24, C:R.26, C:Q.41, C:T.275, C:T.275, C:G.276, C:S.335, C:S.335, C:S.335, C:A.422 Salt bridges: C:R.26, C:R.26 ADP.10: 14 residues within 4Å: Chain D: T.22, R.26, G.274, T.275, G.318, A.319, I.321, Q.322, S.334, S.335, G.418, G.419, A.420 Ligands: MG.12 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:T.22, D:G.274, D:T.275, D:Q.322, D:S.334, D:G.419 Water bridges: D:R.26, D:Q.41, D:Q.41, D:T.275, D:T.275, D:G.276, D:S.335, D:A.422, D:T.447, D:T.447, D:T.447 Salt bridges: D:R.26, D:R.26

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: T.22, Q.91, R.92, E.93, W.112, Y.144, D.253, Q.254, F.278 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.92, A:R.92, A:Y.144, A:Y.144, A:D.253, A:Q.254 Water bridges: A:T.22, A:D.253 GOL.5: 9 residues within 4Å: Chain B: T.22, Q.91, R.92, E.93, W.112, Y.144, D.253, Q.254, F.278 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.92, B:R.92, B:R.92, B:Y.144, B:Q.254 Water bridges: B:T.22, B:D.253 GOL.8: 9 residues within 4Å: Chain C: T.22, Q.91, R.92, E.93, W.112, Y.144, D.253, Q.254, F.278 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:R.92, C:R.92, C:R.92, C:E.93, C:Y.144, C:Q.254 Water bridges: C:T.22, C:T.22, C:D.253 GOL.11: 9 residues within 4Å: Chain D: T.22, Q.91, R.92, E.93, W.112, Y.144, D.253, Q.254, F.278 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.92, D:R.92, D:E.93, D:D.253, D:Q.254 Water bridges: D:T.22, D:T.275

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 7 residues within 4Å: Chain A: G.21, T.22, T.23, S.24, R.26, T.275 Ligands: ADP.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.23, H2O.3 MG.6: 7 residues within 4Å: Chain B: G.21, T.22, T.23, S.24, R.26, T.275 Ligands: ADP.4 No protein-ligand interaction detected (PLIP) MG.9: 7 residues within 4Å: Chain C: G.21, T.22, T.23, S.24, R.26, T.275 Ligands: ADP.7 No protein-ligand interaction detected (PLIP) MG.12: 7 residues within 4Å: Chain D: G.21, T.22, T.23, S.24, R.26, T.275 Ligands: ADP.10 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Phan, J.N. et al., Crystal structure of Glycerol kinase from Elizabethkingia anophelis NUHP1 in complex with ADP and glycerol. TO BE PUBLISHED

Release Date

2019-10-16

Peptides

Glycerol kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Glycerol kinase