SMTL ID : 5lu5.1

A quantum half-site enzyme

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-tetramer

Ligands

4 x M7P: 7-O-phosphono-D-glycero-alpha-D-manno-heptopyranose(Non-covalent)

M7P.1: 15 residues within 4Å: Chain A: N.55, G.56, G.57, S.123, T.124, S.125, S.128, T.171, Q.175 Chain B: A.94, N.97, D.98 Chain D: Q.68, R.72, F.73 19 PLIP interactions: 5 interactions with chain D, 12 interactions with chain A, 2 interactions with chain B Hydrogen bonds: D:Q.68, D:Q.68, D:S.71, D:F.73, A:N.55, A:G.57, A:S.58, A:S.123, A:T.124, A:S.125, A:S.128, A:Q.175, B:N.97, B:D.98 Water bridges: D:R.72, A:N.55, A:N.55, A:T.171, A:T.171 M7P.5: 16 residues within 4Å: Chain A: A.94, N.97, D.98 Chain B: N.55, G.56, G.57, S.123, T.124, S.125, S.128, T.171, Q.175 Chain C: Q.68, S.71, R.72, F.73 19 PLIP interactions: 10 interactions with chain B, 6 interactions with chain C, 3 interactions with chain A Hydrogen bonds: B:N.55, B:G.57, B:S.123, B:T.124, B:S.125, B:S.128, B:Q.175, C:Q.68, C:Q.68, C:S.71, C:F.73, A:N.97, A:D.98 Water bridges: B:N.55, B:N.55, B:S.58, C:R.72, A:D.98 Salt bridges: C:R.72 M7P.9: 15 residues within 4Å: Chain B: Q.68, R.72 Chain C: N.55, G.56, G.57, S.123, T.124, S.125, S.128, T.171, Q.175 Chain D: A.94, N.97, D.98 Ligands: PG4.16 18 PLIP interactions: 12 interactions with chain C, 2 interactions with chain D, 4 interactions with chain B Hydrogen bonds: C:N.55, C:G.57, C:S.123, C:S.123, C:T.124, C:T.124, C:S.125, C:S.128, C:Q.175, D:N.97, D:D.98, B:Q.68, B:Q.68, B:F.73 Water bridges: C:N.55, C:N.55, C:S.58, B:R.72 M7P.14: 16 residues within 4Å: Chain A: Q.68, S.71, R.72, F.73 Chain C: A.94, N.97, D.98 Chain D: N.55, G.56, G.57, S.123, T.124, S.125, S.128, T.171, Q.175 18 PLIP interactions: 2 interactions with chain C, 12 interactions with chain D, 4 interactions with chain A Hydrogen bonds: C:N.97, C:D.98, D:N.55, D:G.57, D:S.58, D:S.123, D:T.124, D:T.124, D:S.125, D:S.128, D:Q.175, A:Q.68, A:S.71, A:F.73 Water bridges: D:N.55, D:N.55, D:T.171, A:R.72

4 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 5 residues within 4Å: Chain A: R.28, A.31, T.32, K.35, L.162 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.35 Water bridges: A:K.35 PG4.8: 4 residues within 4Å: Chain B: A.31, T.32, K.35, L.162 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.35 PG4.15: 3 residues within 4Å: Chain D: N.11, E.15 Ligands: MG.18 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.11 Water bridges: D:E.15, D:E.15 PG4.16: 8 residues within 4Å: Chain C: S.125, K.127, S.128 Chain D: N.97, D.98 Ligands: M7P.9, NA.13, ACT.19 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.125

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

PEG.3: 3 residues within 4Å: Chain A: I.44, I.193, F.194 No protein-ligand interaction detected (PLIP)

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 3 residues within 4Å: Chain A: A.45, Q.46, G.47 No protein-ligand interaction detected (PLIP) PGE.10: 4 residues within 4Å: Chain C: A.31, T.32, K.35, L.162 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.35 PGE.17: 4 residues within 4Å: Chain D: A.31, T.32, K.35, L.162 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.35 Water bridges: D:T.32

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 1 residues within 4Å: Chain B: K.103 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.103 GOL.7: 3 residues within 4Å: Chain B: G.142, T.144, D.161 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.144 Water bridges: B:T.144, B:T.144, B:D.161 GOL.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

NA.13: 2 residues within 4Å: Ligands: PG4.16, ACT.19 1 PLIP interactions: 1 interactions with chain C Water bridges: C:S.125

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.18: 1 residues within 4Å: Ligands: PG4.15 No protein-ligand interaction detected (PLIP)

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

ACT.19: 2 residues within 4Å: Ligands: NA.13, PG4.16 1 PLIP interactions: 1 interactions with chain D Water bridges: D:D.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vivoli, M. et al., A half-site multimeric enzyme achieves its cooperativity without conformational changes. Sci Rep (2017)

Release Date

2017-12-06

Peptides

Phosphoheptose isomerase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Phosphoheptose isomerase