SMTL ID : 5xt4.1

Crystal Structure of Transketolase in complex with TPP intermediate VIII' from Pichia Stipitis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.06 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.175, N.205, I.207 Ligands: T6F.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.175, A:I.207, H2O.5 CA.6: 4 residues within 4Å: Chain B: D.175, N.205, I.207 Ligands: T6F.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.175, B:I.207, H2O.32

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 5 residues within 4Å: Chain A: A.154, A.155, N.158, K.159, P.160 3 PLIP interactions: 3 interactions with chain A Water bridges: A:A.155, A:N.158, A:N.158 PEG.3: 5 residues within 4Å: Chain A: N.330, F.333, Q.348, L.351, D.352 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.330, A:L.351 PEG.4: 5 residues within 4Å: Chain A: K.226, S.227, G.229 Chain B: T.218, D.220 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.226 Water bridges: A:K.258 PEG.7: 5 residues within 4Å: Chain B: A.154, A.155, N.158, K.159, P.160 3 PLIP interactions: 3 interactions with chain B Water bridges: B:A.155, B:N.158, B:N.158 PEG.8: 5 residues within 4Å: Chain B: N.330, F.333, Q.348, L.351, D.352 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.352 Water bridges: B:N.330, B:L.351 PEG.9: 5 residues within 4Å: Chain A: T.218, D.220 Chain B: K.226, S.227, G.229 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.226 Water bridges: B:K.258

2 x T6F: 2-C-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium-2-yl}-6-O-phosphono-D-glucitol(Non-covalent)

T6F.5: 30 residues within 4Å: Chain A: H.47, A.50, H.86, H.120, G.134, P.135, L.136, D.175, G.176, E.180, N.205, I.207, S.208, I.209, I.268, H.281 Chain B: R.376, D.399, L.400, S.403, V.433, E.435, F.459, F.462, Y.465, H.486, D.494, H.498, R.545 Ligands: CA.1 34 PLIP interactions: 17 interactions with chain A, 17 interactions with chain B Hydrogen bonds: A:H.120, A:G.134, A:L.136, A:D.175, A:G.176, A:N.205, A:I.207, A:H.281, B:S.403, B:H.498 Water bridges: A:N.84, A:N.84, A:H.86, A:R.111, A:G.174, A:C.177, B:R.376, B:R.376, B:P.402, B:T.458, B:H.486, B:L.491, B:R.545 Salt bridges: A:H.86, A:H.86, A:H.281, B:R.376, B:H.486, B:R.545 Hydrophobic interactions: B:D.399, B:V.433, B:F.462, B:Y.465 pi-Stacking: B:F.462 T6F.10: 30 residues within 4Å: Chain A: R.376, D.399, L.400, S.403, V.433, E.435, F.459, F.462, Y.465, H.486, D.494, H.498, R.545 Chain B: H.47, A.50, H.86, H.120, G.134, P.135, L.136, D.175, G.176, E.180, N.205, I.207, S.208, I.209, I.268, H.281 Ligands: CA.6 35 PLIP interactions: 18 interactions with chain B, 17 interactions with chain A Hydrogen bonds: B:H.120, B:G.134, B:L.136, B:D.175, B:D.175, B:G.176, B:E.180, B:I.207, B:H.281, A:S.403, A:H.498 Water bridges: B:N.84, B:N.84, B:H.86, B:R.111, B:G.174, B:C.177, A:R.376, A:R.376, A:P.402, A:E.435, A:H.486, A:L.491, A:R.545 Salt bridges: B:H.86, B:H.86, B:H.281, A:R.376, A:H.486, A:R.545 Hydrophobic interactions: A:D.399, A:V.433, A:F.462, A:Y.465 pi-Stacking: A:F.462

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hsu, N.S. et al., Evidence of Diradicals Involved in the Yeast Transketolase Catalyzed Keto-Transferring Reactions. Chembiochem (2018)

Release Date

2018-06-20

Peptides

Transketolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Transketolase

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