SMTL ID : 2ef9.1

Structural and mechanistic changes along an engineered path from metallo to non-metallo KDO8P synthase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.1: 14 residues within 4Å: Chain A: N.11, K.41, S.43, K.46, D.81, Q.99, P.101, A.102, K.124, R.154, H.185, F.220, E.222 Ligands: A5P.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.43, A:A.102 Water bridges: A:N.48, A:F.103, A:Q.127, A:R.154, A:R.154 Salt bridges: A:K.41, A:K.46, A:K.124, A:K.124, A:R.154, A:H.185, A:H.185 PEP.3: 14 residues within 4Å: Chain B: N.11, K.41, S.43, K.46, D.81, Q.99, P.101, A.102, K.124, R.154, H.185, F.220, E.222 Ligands: A5P.4 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.43, B:A.102 Water bridges: B:Q.127, B:R.154 Salt bridges: B:K.41, B:K.46, B:K.124, B:K.124, B:R.154, B:H.185, B:H.185 PEP.5: 14 residues within 4Å: Chain C: N.11, K.41, S.43, K.46, D.81, Q.99, P.101, A.102, K.124, R.154, H.185, F.220, E.222 Ligands: A5P.6 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:S.43, C:A.102 Water bridges: C:N.48, C:F.103, C:Q.127, C:R.154, C:R.154 Salt bridges: C:K.41, C:K.46, C:K.124, C:K.124, C:R.154, C:H.185, C:H.185 PEP.7: 14 residues within 4Å: Chain D: N.11, K.41, S.43, K.46, D.81, Q.99, P.101, A.102, K.124, R.154, H.185, F.220, E.222 Ligands: A5P.8 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:S.43, D:A.102 Water bridges: D:D.81, D:Q.127, D:R.154 Salt bridges: D:K.41, D:K.46, D:K.124, D:K.124, D:R.154, D:H.185, D:H.185

4 x A5P: ARABINOSE-5-PHOSPHATE(Non-covalent)

A5P.2: 13 residues within 4Å: Chain A: N.11, K.46, N.48, R.49, S.50, R.154, H.185, Q.188, K.196, S.197, D.233 Chain B: R.106 Ligands: PEP.1 19 PLIP interactions: 17 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.11, A:K.46, A:K.46, A:N.48, A:S.50, A:S.50, A:Q.188, A:S.197 Water bridges: A:S.51, A:S.54, A:A.102, A:Q.127, A:R.154, A:Q.188, A:D.233, A:D.233, B:R.106 Salt bridges: A:R.49, B:R.106 A5P.4: 12 residues within 4Å: Chain A: R.106 Chain B: N.11, K.46, N.48, R.49, S.50, H.185, Q.188, K.196, S.197, D.233 Ligands: PEP.3 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.11, B:K.46, B:K.46, B:N.48, B:S.50, B:Q.188, B:S.197, B:S.197, B:D.233 Water bridges: B:S.51, B:S.54, B:A.102, B:Q.127, B:R.154, B:S.197 Salt bridges: B:R.49, A:R.106 A5P.6: 13 residues within 4Å: Chain C: N.11, K.46, N.48, R.49, S.50, R.154, H.185, Q.188, K.196, S.197, D.233 Chain D: R.106 Ligands: PEP.5 19 PLIP interactions: 17 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:N.11, C:K.46, C:K.46, C:N.48, C:S.50, C:S.50, C:Q.188, C:S.197 Water bridges: C:S.51, C:S.54, C:A.102, C:Q.127, C:R.154, C:Q.188, C:D.233, C:D.233, D:R.106 Salt bridges: C:R.49, D:R.106 A5P.8: 12 residues within 4Å: Chain C: R.106 Chain D: N.11, K.46, N.48, R.49, S.50, H.185, Q.188, K.196, S.197, D.233 Ligands: PEP.7 17 PLIP interactions: 1 interactions with chain C, 16 interactions with chain D Salt bridges: C:R.106, D:R.49 Hydrogen bonds: D:N.11, D:K.46, D:K.46, D:N.48, D:S.50, D:Q.188, D:S.197, D:S.197, D:D.233 Water bridges: D:S.51, D:S.54, D:A.102, D:Q.127, D:R.154, D:S.197

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kona, F. et al., Structural and Mechanistic Changes along an Engineered Path from Metallo to Nonmetallo 3-Deoxy-d-manno-octulosonate 8-Phosphate Synthases. Biochemistry (2007)

Release Date

2007-04-24

Peptides

2-dehydro-3-deoxyphosphooctonate aldolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

2-dehydro-3-deoxyphosphooctonate aldolase