SMTL ID : 5xrv.1

Crystal Structure of Transketolase in complex with TPP_V and fructose-6-phosphate from Pichia Stipitis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.175, N.205, I.207 Ligands: 8EF.3, TPP.10 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.175, A:I.207, H2O.7 CA.11: 5 residues within 4Å: Chain B: D.175, N.205, I.207 Ligands: 8EF.13, TPP.20 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.175, B:I.207, H2O.42

2 x F6R: FRUCTOSE -6-PHOSPHATE(Non-covalent)

F6R.2: 16 residues within 4Å: Chain A: H.47, H.86, H.120, G.134, I.209, H.281 Chain B: R.376, L.400, S.403, F.459, H.486, D.494, H.498, R.545 Ligands: 8EF.3, TPP.10 15 PLIP interactions: 5 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:H.120, A:H.281, B:S.403 Water bridges: A:H.86, A:R.111, A:H.281, B:R.376, B:R.376, B:R.376, B:R.376, B:H.486, B:L.491 Salt bridges: B:R.376, B:H.486, B:R.545 F6R.12: 16 residues within 4Å: Chain A: R.376, L.400, S.403, F.459, H.486, D.494, H.498, R.545 Chain B: H.47, H.86, H.120, G.134, I.209, H.281 Ligands: 8EF.13, TPP.20 15 PLIP interactions: 10 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:S.403, B:H.120, B:H.281 Water bridges: A:R.376, A:R.376, A:R.376, A:R.376, A:H.486, A:L.491, B:H.86, B:R.111, B:H.281 Salt bridges: A:R.376, A:H.486, A:R.545

2 x 8EF: 2-[(5S)-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methylidene-1,3-thiazolidin-5-yl]ethyl phosphono hydrogen phosphate(Non-covalent)

8EF.3: 24 residues within 4Å: Chain A: A.50, H.86, 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: D.399, L.400, V.433, E.435, F.462, Y.465, H.498 Ligands: CA.1, F6R.2, TPP.10 20 PLIP interactions: 15 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:I.209, A:I.209, B:D.399, B:F.462, B:Y.465 Hydrogen bonds: A:G.134, A:L.136, A:D.175, A:G.176, A:N.205, A:N.205 Water bridges: A:N.84, A:N.84, A:H.86, A:C.177, B:T.458 Salt bridges: A:H.86, A:H.86, A:H.281 pi-Stacking: B:F.462 8EF.13: 24 residues within 4Å: Chain A: D.399, L.400, V.433, E.435, F.462, Y.465, H.498 Chain B: A.50, H.86, 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.11, F6R.12, TPP.20 23 PLIP interactions: 18 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.209, B:I.209, A:D.399, A:F.462, A:Y.465 Hydrogen bonds: B:G.134, B:L.136, B:D.175, B:D.175, B:G.176, B:E.180, B:N.205 Water bridges: B:N.84, B:N.84, B:H.86, B:G.174, B:C.177, B:H.281, A:E.435 Salt bridges: B:H.86, B:H.86, B:H.281 pi-Stacking: A:F.462

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

PEG.4: 3 residues within 4Å: Chain A: A.154, N.158, K.159 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.158 Water bridges: A:A.155, A:K.159 PEG.5: 4 residues within 4Å: Chain A: Q.546, A.659, P.660, F.663 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.546 PEG.6: 5 residues within 4Å: Chain A: N.330, F.333, Q.348, L.351, D.352 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.351 Water bridges: A:Q.326, A:N.330, A:N.330, A:Q.348 PEG.7: 4 residues within 4Å: Chain A: K.226, H.231, I.232, E.234 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.226, A:H.231, A:I.232 Water bridges: A:K.226, A:E.234 PEG.8: 4 residues within 4Å: Chain A: K.226, S.227, G.229 Chain B: T.218 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:D.220 Hydrogen bonds: A:S.227 PEG.9: 4 residues within 4Å: Chain A: V.104, E.105, K.108, S.304 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.105, A:K.108 Water bridges: A:E.105 PEG.14: 3 residues within 4Å: Chain B: A.154, N.158, K.159 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.158 Water bridges: B:A.155, B:K.159 PEG.15: 4 residues within 4Å: Chain B: Q.546, A.659, P.660, F.663 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.546 PEG.16: 5 residues within 4Å: Chain B: N.330, F.333, Q.348, L.351, D.352 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.351, B:D.352 Water bridges: B:Q.326, B:N.330, B:N.330, B:Q.348 PEG.17: 4 residues within 4Å: Chain B: K.226, H.231, I.232, E.234 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.226, B:I.232 Water bridges: B:K.226, B:H.231 PEG.18: 4 residues within 4Å: Chain A: T.218 Chain B: K.226, S.227, G.229 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.227 PEG.19: 4 residues within 4Å: Chain B: V.104, E.105, K.108, S.304 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.105, B:K.108

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.10: 25 residues within 4Å: Chain A: A.50, H.86, G.134, P.135, L.136, G.174, D.175, G.176, E.180, N.205, I.207, S.208, I.209, I.268, H.281 Chain B: D.399, L.400, V.433, E.435, F.462, Y.465, H.498 Ligands: CA.1, F6R.2, 8EF.3 22 PLIP interactions: 6 interactions with chain B, 16 interactions with chain A Hydrophobic interactions: B:D.399, B:L.400, B:F.462, B:Y.465, A:L.136, A:I.209, A:I.209 Water bridges: B:T.458, A:A.50, A:N.84, A:N.84, A:C.177 pi-Stacking: B:F.462 Hydrogen bonds: A:G.134, A:L.136, A:D.175, A:G.176, A:N.205, A:I.207 Salt bridges: A:H.86, A:H.86, A:H.281 TPP.20: 25 residues within 4Å: Chain A: D.399, L.400, V.433, E.435, F.462, Y.465, H.498 Chain B: A.50, H.86, G.134, P.135, L.136, G.174, D.175, G.176, E.180, N.205, I.207, S.208, I.209, I.268, H.281 Ligands: CA.11, F6R.12, 8EF.13 24 PLIP interactions: 18 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:L.136, B:I.209, B:I.209, A:D.399, A:L.400, A:F.462, A:Y.465 Hydrogen bonds: B:G.134, B:L.136, B:D.175, B:D.175, B:G.176, B:E.180, B:N.205, B:I.207 Water bridges: B:A.50, B:N.84, B:N.84, B:C.177, A:E.435 Salt bridges: B:H.86, B:H.86, B:H.281 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

2018-06-13

Peptides

Transketolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Transketolase

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