SMTL ID : 6yr3.1

1.48 Angstrom Resolution Crystal Structure of Transaldolase from Thermoplasma acidophilum in complex with D-fructose 6-phosphate Schiff-base intermediate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 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 18 PLIP interactions: 18 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 Water bridges: A:T.110, A:I.168, A:R.169, A:R.169 Salt bridges: A:R.135, A:R.169 F6R.5: 15 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 17 PLIP interactions: 17 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:K.86, B:N.108, B:S.130, B:S.130, B:S.167, B:S.167, B:S.167 Water bridges: B:T.110, B:I.168 Salt bridges: B:R.135, B:R.169 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.11: 15 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, R.169 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:K.86 Hydrogen bonds: D:D.6, D:T.26, D:N.28, D:K.86, 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, D:R.169 F6R.13: 14 residues within 4Å: 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 16 PLIP interactions: 16 interactions with chain E Hydrophobic interactions: E:K.86 Hydrogen bonds: E:D.6, E:T.26, E:N.28, E:K.86, E:T.110, E:S.130, E:S.130, E:S.167, E:S.167, E:S.167 Water bridges: E:R.135, E:R.135, 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 16 PLIP interactions: 16 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 Water bridges: F:I.168, F:R.169, F:R.169 Salt bridges: F:R.135, F:R.169 F6R.21: 15 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 15 PLIP interactions: 15 interactions with chain G Hydrophobic interactions: G:K.86 Hydrogen bonds: G:D.6, G:T.26, G:N.28, G:K.86, G:K.86, G:N.108, G:S.130, G:S.130, G:S.167, G:S.167, G:S.167 Water bridges: G:I.168 Salt bridges: G:R.135, G:R.169 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.27: 15 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, R.169 15 PLIP interactions: 15 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: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, I:R.169 F6R.29: 14 residues within 4Å: 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 17 PLIP interactions: 17 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:R.135, J:R.135, J:I.168 Salt bridges: J:R.135, J:R.169

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 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.30 5 PLIP interactions: 3 interactions with chain J, 2 interactions with chain A Hydrogen bonds: J:N.170, 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.28 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: 12 residues within 4Å: Chain C: M.144, N.170, I.172, H.173, R.176 Chain H: D.137, M.144, N.170, I.172, H.173, R.176 Ligands: GOL.25 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain H Hydrogen bonds: C:N.170, C:R.176, H:N.170, H:R.176 GOL.12: 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: 3 interactions with chain G, 2 interactions with chain D Hydrogen bonds: G:N.170, G:H.173, G:R.176, D:N.170, D:R.176 GOL.14: 11 residues within 4Å: Chain E: D.137, N.170, I.172, H.173, R.176 Chain F: M.144, N.170, I.172, H.173, R.176 Ligands: GOL.18 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:N.170, F:N.170, F:R.176, E:N.170, E:R.176 GOL.18: 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.14 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:N.170, F:R.176, E:N.170, E:N.170, E: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.12 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: 12 residues within 4Å: Chain C: D.137, M.144, N.170, I.172, H.173, R.176 Chain H: M.144, N.170, I.172, H.173, R.176 Ligands: GOL.9 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.28: 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: 3 interactions with chain B, 2 interactions with chain I Hydrogen bonds: B:N.170, B:H.173, B:R.176, I:N.170, I:R.176 GOL.30: 11 residues within 4Å: Chain A: M.144, N.170, I.172, H.173, R.176 Chain J: D.137, N.170, I.172, H.173, R.176 Ligands: GOL.2 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain J Hydrogen bonds: A:N.170, A:N.170, A:R.176, J:N.170, J:R.176

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

ACT.3: 5 residues within 4Å: Chain A: M.1 Chain E: L.119, K.123, Y.157, I.159 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain E Hydrogen bonds: A:M.1 Hydrophobic interactions: E:K.123, E:I.159 Water bridges: E:K.123, E:K.123 Salt bridges: E:K.123 ACT.4: 4 residues within 4Å: Chain A: M.144, D.148, R.176, I.180 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.176 ACT.7: 4 residues within 4Å: Chain B: R.169, N.170 Chain I: R.169, N.170 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain I Hydrogen bonds: B:N.170, I:N.170 Salt bridges: B:H.173, I:H.173 Hydrophobic interactions: I:R.169 Water bridges: I:R.169 ACT.10: 5 residues within 4Å: Chain C: R.169, N.170 Chain H: R.169, N.170 Ligands: ACT.26 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain H Hydrophobic interactions: C:R.169 Hydrogen bonds: C:N.170, H:N.170 ACT.15: 4 residues within 4Å: Chain E: R.169, N.170 Chain F: R.169, N.170 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:R.169 Hydrogen bonds: E:N.170, F:N.170 Salt bridges: E:H.173 ACT.16: 3 residues within 4Å: Chain E: M.144, R.176, I.180 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:M.144 Salt bridges: E:R.176 ACT.19: 5 residues within 4Å: Chain F: M.1 Chain J: L.119, K.123, Y.157, I.159 6 PLIP interactions: 1 interactions with chain F, 5 interactions with chain J Hydrogen bonds: F:M.1 Hydrophobic interactions: J:K.123, J:I.159 Water bridges: J:K.123, J:K.123 Salt bridges: J:K.123 ACT.20: 4 residues within 4Å: Chain F: M.144, D.148, R.176, I.180 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:R.176 ACT.23: 4 residues within 4Å: Chain D: R.169, N.170 Chain G: R.169, N.170 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain G Hydrophobic interactions: D:R.169 Hydrogen bonds: D:N.170, G:N.170 Water bridges: D:R.169 Salt bridges: D:H.173, G:H.173 ACT.26: 5 residues within 4Å: Chain C: R.169, N.170 Chain H: R.169, N.170 Ligands: ACT.10 3 PLIP interactions: 1 interactions with chain H, 2 interactions with chain C Hydrogen bonds: H:N.170, C:N.170 Hydrophobic interactions: C:R.169 ACT.31: 4 residues within 4Å: Chain A: R.169, N.170 Chain J: R.169, N.170 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain A Hydrophobic interactions: J:R.169 Hydrogen bonds: J:N.170, A:N.170 Salt bridges: J:H.173 ACT.32: 3 residues within 4Å: Chain J: M.144, R.176, I.180 3 PLIP interactions: 3 interactions with chain J Hydrophobic interactions: J:M.144 Water bridges: J:D.148 Salt bridges: J:R.176

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

2021-04-28

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

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