SMTL ID : 5za0.1

A cryo-protectant induces the conformational change of glyceraldehyde-3-phosphate dehydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x GLC- GLC: alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.1: 7 residues within 4Å: Chain A: H.191, K.192, D.193, W.194, R.195 Chain B: D.278, K.296 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:H.191, A:W.194 Hydrogen bonds: B:D.278 GLC-GLC.3: 7 residues within 4Å: Chain A: D.278, K.296 Chain B: H.191, K.192, D.193, W.194, R.195 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:H.191, B:W.194 Hydrogen bonds: A:D.278 GLC-GLC.5: 7 residues within 4Å: Chain C: H.191, K.192, D.193, W.194, R.195 Chain D: D.278, K.296 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Water bridges: C:H.191, C:W.194 Hydrogen bonds: D:D.278 GLC-GLC.7: 7 residues within 4Å: Chain C: D.278, K.296 Chain D: H.191, K.192, D.193, W.194, R.195 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Water bridges: D:H.191, D:W.194 Hydrogen bonds: C:D.278

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 7 residues within 4Å: Chain A: V.131, K.132, G.133, A.134, N.135, F.136, D.137 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.133, A:N.135, A:F.136, A:D.137 SO4.4: 7 residues within 4Å: Chain B: V.131, K.132, G.133, A.134, N.135, F.136, D.137 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.133, B:N.135, B:F.136, B:D.137 SO4.6: 7 residues within 4Å: Chain C: V.131, K.132, G.133, A.134, N.135, F.136, D.137 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.133, C:N.135, C:F.136, C:D.137 SO4.8: 7 residues within 4Å: Chain D: V.131, K.132, G.133, A.134, N.135, F.136, D.137 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.133, D:N.135, D:F.136, D:D.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y.J., A cryoprotectant induces conformational change in glyceraldehyde-3-phosphate dehydrogenase. Acta Crystallogr F Struct Biol Commun (2018)

Release Date

2018-05-30

Peptides

Glyceraldehyde-3-phosphate dehydrogenase A: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Glyceraldehyde-3-phosphate dehydrogenase A

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