SMTL ID : 3s1w.1

Transaldolase variant Lys86Ala from Thermoplasma acidophilum in complex with glycerol and citrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-10-mer

Ligands

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 12 residues within 4Å: Chain A: D.6, T.26, T.27, N.28, L.31, N.108, T.110, S.130, F.132, L.164, A.166 Ligands: FLC.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.6, A:T.27, A:N.28, A:N.108, A:S.130, A:S.130 Water bridges: A:T.27 GOL.3: 12 residues within 4Å: Chain B: D.6, T.26, T.27, N.28, L.31, N.108, T.110, S.130, F.132, L.164, A.166 Ligands: FLC.4 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.6, B:N.28, B:N.108, B:S.130, B:S.130 Water bridges: B:T.27, B:T.27 GOL.5: 12 residues within 4Å: Chain C: D.6, T.26, T.27, N.28, L.31, N.108, T.110, S.130, F.132, L.164, A.166 Ligands: FLC.6 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:D.6, C:T.26, C:T.27, C:N.28, C:N.108, C:S.130, C:S.130 Water bridges: C:T.27 GOL.7: 12 residues within 4Å: Chain D: D.6, T.26, T.27, N.28, L.31, N.108, T.110, S.130, F.132, L.164, A.166 Ligands: FLC.8 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:D.6, D:T.27, D:N.28, D:N.108, D:S.130, D:S.130 Water bridges: D:T.27 GOL.9: 12 residues within 4Å: Chain E: D.6, T.26, T.27, N.28, L.31, N.108, T.110, S.130, F.132, L.164, A.166 Ligands: FLC.10 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:T.27, E:N.28, E:N.108, E:S.130, E:S.130 GOL.11: 12 residues within 4Å: Chain F: D.6, T.26, T.27, N.28, L.31, N.108, T.110, S.130, F.132, L.164, A.166 Ligands: FLC.12 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:D.6, F:T.27, F:N.28, F:N.108, F:S.130, F:S.130 Water bridges: F:T.27 GOL.13: 12 residues within 4Å: Chain G: D.6, T.26, T.27, N.28, L.31, N.108, T.110, S.130, F.132, L.164, A.166 Ligands: FLC.14 7 PLIP interactions: 7 interactions with chain G Hydrogen bonds: G:D.6, G:N.28, G:N.108, G:S.130, G:S.130 Water bridges: G:T.27, G:T.27 GOL.15: 12 residues within 4Å: Chain H: D.6, T.26, T.27, N.28, L.31, N.108, T.110, S.130, F.132, L.164, A.166 Ligands: FLC.16 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: H:D.6, H:T.27, H:N.28, H:N.108, H:S.130, H:S.130 Water bridges: H:T.27 GOL.17: 12 residues within 4Å: Chain I: D.6, T.26, T.27, N.28, L.31, N.108, T.110, S.130, F.132, L.164, A.166 Ligands: FLC.18 7 PLIP interactions: 7 interactions with chain I Hydrogen bonds: I:D.6, I:T.27, I:N.28, I:N.108, I:S.130, I:S.130 Water bridges: I:T.27 GOL.19: 12 residues within 4Å: Chain J: D.6, T.26, T.27, N.28, L.31, N.108, T.110, S.130, F.132, L.164, A.166 Ligands: FLC.20 5 PLIP interactions: 5 interactions with chain J Hydrogen bonds: J:T.27, J:N.28, J:N.108, J:S.130, J:S.130

10 x FLC: CITRATE ANION(Non-covalent)

FLC.2: 6 residues within 4Å: Chain A: D.6, F.132, R.135, S.167, R.169 Ligands: GOL.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.6, A:R.135, A:S.167 Water bridges: A:R.135, A:I.168, A:R.169, A:R.169 Salt bridges: A:R.135, A:R.135, A:R.169, A:R.169 FLC.4: 6 residues within 4Å: Chain B: D.6, F.132, R.135, S.167, R.169 Ligands: GOL.3 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.135, B:S.167 Water bridges: B:I.168, B:R.169, B:R.169, B:R.169 Salt bridges: B:R.135, B:R.135, B:R.169, B:R.169 FLC.6: 6 residues within 4Å: Chain C: D.6, F.132, R.135, S.167, R.169 Ligands: GOL.5 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:D.6, C:R.135, C:S.167 Water bridges: C:R.135, C:I.168, C:R.169 Salt bridges: C:R.135, C:R.135, C:R.169, C:R.169 FLC.8: 6 residues within 4Å: Chain D: D.6, F.132, R.135, S.167, R.169 Ligands: GOL.7 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:R.135, D:S.167 Water bridges: D:D.6, D:R.135, D:I.168, D:R.169, D:R.169, D:R.169 Salt bridges: D:R.135, D:R.135, D:R.169, D:R.169 FLC.10: 6 residues within 4Å: Chain E: D.6, F.132, R.135, S.167, R.169 Ligands: GOL.9 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:R.135, E:S.167 Water bridges: E:I.168, E:R.169, E:R.169, E:R.169 Salt bridges: E:R.135, E:R.135, E:R.169, E:R.169 FLC.12: 6 residues within 4Å: Chain F: D.6, F.132, R.135, S.167, R.169 Ligands: GOL.11 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:D.6, F:R.135, F:S.167 Water bridges: F:R.135, F:I.168, F:R.169, F:R.169 Salt bridges: F:R.135, F:R.135, F:R.169, F:R.169 FLC.14: 6 residues within 4Å: Chain G: D.6, F.132, R.135, S.167, R.169 Ligands: GOL.13 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:R.135, G:S.167 Water bridges: G:I.168, G:R.169, G:R.169, G:R.169 Salt bridges: G:R.135, G:R.135, G:R.169, G:R.169 FLC.16: 6 residues within 4Å: Chain H: D.6, F.132, R.135, S.167, R.169 Ligands: GOL.15 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:D.6, H:R.135, H:S.167 Water bridges: H:R.135, H:I.168, H:R.169 Salt bridges: H:R.135, H:R.135, H:R.169, H:R.169 FLC.18: 6 residues within 4Å: Chain I: D.6, F.132, R.135, S.167, R.169 Ligands: GOL.17 11 PLIP interactions: 11 interactions with chain I Hydrogen bonds: I:R.135, I:S.167 Water bridges: I:R.135, I:I.168, I:R.169, I:R.169, I:R.169 Salt bridges: I:R.135, I:R.135, I:R.169, I:R.169 FLC.20: 6 residues within 4Å: Chain J: D.6, F.132, R.135, S.167, R.169 Ligands: GOL.19 10 PLIP interactions: 10 interactions with chain J Hydrogen bonds: J:R.135, J:S.167 Water bridges: J:I.168, J:R.169, J:R.169, J:R.169 Salt bridges: J:R.135, J:R.135, J:R.169, J:R.169

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lehwess-Litzmann, A. et al., Twisted Schiff base intermediates and substrate locale revise transaldolase mechanism. Nat.Chem.Biol. (2011)

Release Date

2011-08-24

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