SMTL ID : 6yrm.1

Transaldolase variant T30A from T. acidophilum in complex with D-fructose 6-phosphate Schiff-base intermediate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-10-mer

Ligands

10 x F6R: FRUCTOSE -6-PHOSPHATE(Covalent)

F6R.1: 15 residues within 4Å: Chain A: D.6, T.26, T.27, N.28, L.31, K.86, N.108, T.110, S.130, F.132, R.135, L.164, A.166, S.167, R.169 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:K.86 Hydrogen bonds: A:D.6, A:T.26, A:T.26, A:N.28, A:K.86, A:N.108, A:S.130, A:S.130, A:S.167, A:S.167, A:S.167, A:R.169 Water bridges: A:T.110, A:I.168 Salt bridges: A:R.135 F6R.5: 16 residues within 4Å: Chain B: D.6, T.26, T.27, N.28, L.31, K.86, N.108, T.110, S.130, F.132, R.135, L.164, A.166, S.167, R.169 Chain C: F.208 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:K.86 Hydrogen bonds: B:D.6, B:T.26, B:T.26, B:N.28, B:K.86, B:N.108, B:S.130, B:S.130, B:S.167, B:S.167, B:S.167, B:R.169 Water bridges: B:T.110, B:I.168 Salt bridges: B:R.135 F6R.8: 15 residues within 4Å: Chain C: D.6, T.26, T.27, N.28, L.31, K.86, N.108, T.110, S.130, F.132, R.135, L.164, A.166, S.167 Chain D: F.208 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:K.86 Hydrogen bonds: C:D.6, C:T.26, C:T.26, C:N.28, C:K.86, C:N.108, C:S.130, C:S.130, C:S.167 Water bridges: C:I.168, C:R.169, C:R.169 Salt bridges: C:R.135 F6R.12: 14 residues within 4Å: Chain D: D.6, T.26, T.27, N.28, L.31, K.86, N.108, T.110, S.130, F.132, R.135, L.164, A.166, S.167 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:K.86 Hydrogen bonds: D:D.6, D:T.26, D:N.28, D:K.86, D:N.108, D:S.130, D:S.130, D:S.167 Water bridges: D:I.168 Salt bridges: D:R.135 F6R.14: 15 residues within 4Å: Chain A: F.208 Chain E: D.6, T.26, T.27, N.28, L.31, K.86, N.108, T.110, S.130, F.132, R.135, A.166, S.167, R.169 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:K.86 Hydrogen bonds: E:D.6, E:T.26, E:N.28, E:K.86, E:K.86, E:T.110, E:S.130, E:S.130, E:S.167, E:S.167, E:S.167 Water bridges: E:I.168 Salt bridges: E:R.135, E:R.169 F6R.17: 15 residues within 4Å: Chain F: D.6, T.26, T.27, N.28, L.31, K.86, N.108, T.110, S.130, F.132, R.135, L.164, A.166, S.167, R.169 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:K.86 Hydrogen bonds: F:D.6, F:T.26, F:N.28, F:K.86, F:N.108, F:S.130, F:S.130, F:S.167, F:S.167, F:S.167, F:R.169 Water bridges: F:I.168 Salt bridges: F:R.135 F6R.21: 16 residues within 4Å: Chain G: D.6, T.26, T.27, N.28, L.31, K.86, N.108, T.110, S.130, F.132, R.135, L.164, A.166, S.167, R.169 Chain H: F.208 14 PLIP interactions: 14 interactions with chain G Hydrophobic interactions: G:K.86 Hydrogen bonds: G:D.6, G:T.26, G:N.28, G:K.86, G:N.108, G:S.130, G:S.130, G:S.167, G:S.167, G:S.167, G:R.169 Water bridges: G:I.168 Salt bridges: G:R.135 F6R.24: 15 residues within 4Å: Chain H: D.6, T.26, T.27, N.28, L.31, K.86, N.108, T.110, S.130, F.132, R.135, L.164, A.166, S.167 Chain I: F.208 14 PLIP interactions: 14 interactions with chain H Hydrophobic interactions: H:K.86 Hydrogen bonds: H:D.6, H:T.26, H:N.28, H:K.86, H:N.108, H:S.130, H:S.130, H:S.167 Water bridges: H:T.110, H:I.168, H:R.169, H:R.169 Salt bridges: H:R.135 F6R.28: 14 residues within 4Å: Chain I: D.6, T.26, T.27, N.28, L.31, K.86, N.108, T.110, S.130, F.132, R.135, L.164, A.166, S.167 13 PLIP interactions: 13 interactions with chain I Hydrophobic interactions: I:K.86 Hydrogen bonds: I:D.6, I:T.26, I:T.26, I:N.28, I:K.86, I:N.108, I:S.130, I:S.130, I:S.167 Water bridges: I:T.110, I:I.168 Salt bridges: I:R.135 F6R.30: 15 residues within 4Å: Chain F: F.208 Chain J: D.6, T.26, T.27, N.28, L.31, K.86, N.108, T.110, S.130, F.132, R.135, A.166, S.167, R.169 15 PLIP interactions: 15 interactions with chain J Hydrophobic interactions: J:K.86 Hydrogen bonds: J:D.6, J:T.26, J:T.26, J:N.28, J:K.86, J:S.130, J:S.130, J:S.167, J:S.167, J:S.167 Water bridges: J:T.110, J:I.168 Salt bridges: J:R.135, J:R.169

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: D.142 Chain I: M.149 Chain J: L.175, R.176, V.179 3 PLIP interactions: 1 interactions with chain J, 1 interactions with chain A, 1 interactions with chain I Hydrogen bonds: J:R.176, A:D.142 Water bridges: I:Q.145 GOL.3: 11 residues within 4Å: Chain A: D.137, M.144, N.170, I.172, H.173, R.176 Chain J: N.170, I.172, H.173, R.176 Ligands: GOL.31 4 PLIP interactions: 2 interactions with chain J, 2 interactions with chain A Hydrogen bonds: J:N.170, J:R.176, A:N.170, A:R.176 GOL.6: 11 residues within 4Å: Chain B: N.170, I.172, H.173, R.176 Chain I: D.137, M.144, N.170, I.172, H.173, R.176 Ligands: GOL.29 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain I Hydrogen bonds: B:N.170, B:N.170, B:R.176, I:N.170, I:R.176 GOL.9: 6 residues within 4Å: Chain B: M.149 Chain C: L.175, R.176, V.179 Chain H: D.142, Q.145 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain H Hydrogen bonds: C:R.176, H:Q.145 Water bridges: H:Q.145 GOL.10: 11 residues within 4Å: Chain C: N.170, I.172, H.173, R.176 Chain H: D.137, M.144, N.170, I.172, H.173, R.176 Ligands: GOL.26 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain C Hydrogen bonds: H:N.170, H:R.176, C:N.170, C:R.176 GOL.13: 11 residues within 4Å: Chain D: M.144, N.170, I.172, H.173, R.176 Chain G: D.137, N.170, I.172, H.173, R.176 Ligands: GOL.22 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain G Hydrogen bonds: D:N.170, D:R.176, G:N.170, G:H.173, G:R.176 GOL.15: 12 residues within 4Å: Chain E: D.137, M.144, N.170, I.172, H.173, R.176 Chain F: M.144, N.170, I.172, H.173, R.176 Ligands: GOL.19 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:N.170, E:R.176, F:N.170, F:R.176 GOL.18: 5 residues within 4Å: Chain D: M.149 Chain E: L.175, R.176, V.179 Chain F: D.142 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:R.176 Water bridges: D:Q.145 GOL.19: 11 residues within 4Å: Chain E: N.170, I.172, H.173, R.176 Chain F: D.137, M.144, N.170, I.172, H.173, R.176 Ligands: GOL.15 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:N.170, E:R.176, F:N.170, F:R.176 GOL.22: 11 residues within 4Å: Chain D: D.137, M.144, N.170, I.172, H.173, R.176 Chain G: N.170, I.172, H.173, R.176 Ligands: GOL.13 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain G Hydrogen bonds: D:N.170, D:R.176, G:N.170, G:N.170, G:R.176 GOL.25: 6 residues within 4Å: Chain C: D.142, Q.145 Chain G: M.149 Chain H: L.175, R.176, V.179 4 PLIP interactions: 1 interactions with chain H, 3 interactions with chain C Hydrogen bonds: H:R.176, C:D.142, C:Q.145 Water bridges: C:Q.145 GOL.26: 11 residues within 4Å: Chain C: D.137, M.144, N.170, I.172, H.173, R.176 Chain H: N.170, I.172, H.173, R.176 Ligands: GOL.10 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain C Hydrogen bonds: H:N.170, H:R.176, C:N.170, C:R.176 GOL.29: 11 residues within 4Å: Chain B: D.137, N.170, I.172, H.173, R.176 Chain I: M.144, N.170, I.172, H.173, R.176 Ligands: GOL.6 5 PLIP interactions: 2 interactions with chain I, 3 interactions with chain B Hydrogen bonds: I:N.170, I:R.176, B:N.170, B:H.173, B:R.176 GOL.31: 12 residues within 4Å: Chain A: M.144, N.170, I.172, H.173, R.176 Chain J: D.137, M.144, N.170, I.172, H.173, R.176 Ligands: GOL.3 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain J Hydrogen bonds: A:N.170, A:R.176, J:N.170, J:R.176

8 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 5 residues within 4Å: Chain A: M.1 Chain E: L.119, K.123, Y.157, I.159 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:M.1 Hydrophobic interactions: E:I.159 Salt bridges: E:K.123 ACT.7: 4 residues within 4Å: Chain B: R.169, N.170 Chain I: R.169, N.170 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain I Hydrophobic interactions: B:R.169 Hydrogen bonds: B:N.170, I:N.170 Water bridges: B:D.138, B:R.169, B:R.169 Salt bridges: B:H.173 ACT.11: 5 residues within 4Å: Chain C: R.169, N.170 Chain H: R.169, N.170 Ligands: ACT.27 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain H Hydrogen bonds: C:N.170, H:N.170 Water bridges: C:R.169 Hydrophobic interactions: H:R.169 ACT.16: 4 residues within 4Å: Chain E: R.169, N.170 Chain F: R.169, N.170 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: F:R.169 Hydrogen bonds: F:N.170, E:N.170 Water bridges: E:R.169 Salt bridges: E:H.173 ACT.20: 5 residues within 4Å: Chain F: M.1 Chain J: L.119, K.123, Y.157, I.159 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain F Hydrophobic interactions: J:I.159 Salt bridges: J:K.123 Hydrogen bonds: F:M.1 ACT.23: 4 residues within 4Å: Chain D: R.169, N.170 Chain G: R.169, N.170 7 PLIP interactions: 5 interactions with chain G, 2 interactions with chain D Hydrophobic interactions: G:R.169 Hydrogen bonds: G:N.170, D:N.170 Water bridges: G:D.138, G:R.169, D:R.169 Salt bridges: G:H.173 ACT.27: 5 residues within 4Å: Chain C: R.169, N.170 Chain H: R.169, N.170 Ligands: ACT.11 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain H Hydrophobic interactions: C:R.169 Hydrogen bonds: C:N.170, H:N.170 Water bridges: H:R.169 ACT.32: 4 residues within 4Å: Chain A: R.169, N.170 Chain J: R.169, N.170 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain J Hydrophobic interactions: A:R.169 Hydrogen bonds: A:N.170, J:N.170 Water bridges: J:R.169 Salt bridges: J:H.173

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sautner, V. et al., Large-scale motions underlie physical but not chemical steps in transaldolase mechanism: Substrate binding by conformational selection and rate-determining product release. To Be Published

Release Date

2021-05-12

Peptides

Probable transaldolase: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
A

G
B

H
C

I
D

J
E

Probable transaldolase