SMTL ID : 4ff7.1

Structure of C126S mutant of Saccharomyces cerevisiae triosephosphate isomerase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

1 x PGA: 2-PHOSPHOGLYCOLIC ACID(Non-covalent)

PGA.1: 11 residues within 4Å: Chain A: K.12, H.95, E.165, A.169, I.170, G.171, S.211, L.230, G.232, G.233 Ligands: NA.8 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.171, A:G.210, A:S.211, A:G.232, A:G.233 Water bridges: A:K.12, A:G.173, A:A.212 Salt bridges: A:K.12, A:K.12, A:H.95

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: K.17, D.48, Y.49 Chain B: K.17, D.48, Y.49, S.52 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:K.17, B:K.17, B:D.48, B:S.52, B:S.52 GOL.3: 4 residues within 4Å: Chain A: E.153, V.154, K.155, D.156 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.153, A:K.155, A:D.156, A:D.156 GOL.4: 4 residues within 4Å: Chain A: K.69, A.70, S.71, F.115 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.70, A:S.71, A:S.71 GOL.5: 7 residues within 4Å: Chain A: Y.101, F.102, H.103 Chain B: F.102, H.103, D.105, F.108 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.105 GOL.6: 2 residues within 4Å: Chain A: R.26, P.238 No protein-ligand interaction detected (PLIP) GOL.7: 5 residues within 4Å: Chain A: K.89, W.90, V.121, G.122, N.159 No protein-ligand interaction detected (PLIP) GOL.11: 10 residues within 4Å: Chain B: N.10, K.12, H.95, E.165, G.209, G.210, L.230, V.231, G.232 Ligands: SO4.9 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.10, B:K.12, B:E.165, B:E.165 Water bridges: B:E.97, B:S.211 GOL.12: 5 residues within 4Å: Chain A: H.103, D.105, F.108 Chain B: Y.101, H.103 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:F.102, A:D.105, B:H.103 GOL.13: 5 residues within 4Å: Chain B: V.54, K.55, K.56, P.57 Ligands: GOL.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.54 GOL.14: 3 residues within 4Å: Chain B: K.55, P.57 Ligands: GOL.13 No protein-ligand interaction detected (PLIP) GOL.15: 4 residues within 4Å: Chain B: E.25, N.28, T.29, K.55 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.28 Water bridges: B:L.53 GOL.16: 4 residues within 4Å: Chain B: S.96, E.97, S.100, I.170 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.96, B:S.100, B:S.100 Water bridges: B:E.97

1 x NA: SODIUM ION(Non-functional Binders)

NA.8: 5 residues within 4Å: Chain A: N.10, H.95, E.165, L.230 Ligands: PGA.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.10

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.9: 4 residues within 4Å: Chain B: S.211, G.232, G.233 Ligands: GOL.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.233 Water bridges: B:G.232, B:G.232, B:A.234 SO4.10: 2 residues within 4Å: Chain B: A.30, S.31 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.31

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.17: 5 residues within 4Å: Chain B: K.89, W.90, G.120, G.122, N.159 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.120, B:G.122 PO4.18: 4 residues within 4Å: Chain B: K.69, A.70, S.71, F.115 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.70, B:S.71, B:S.71 PO4.19: 4 residues within 4Å: Chain B: P.33, E.34, N.35, V.36 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.34, B:N.35, B:N.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hernandez-Santoyo, A. et al., Effects of a buried cysteine-to-serine mutation on yeast triosephosphate isomerase structure and stability. Int J Mol Sci (2012)

Release Date

2012-08-22

Peptides

Triosephosphate isomerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Triosephosphate isomerase