SMTL ID : 2nxh.2 (2 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-tetramer

Ligands

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

PO4.1: 3 residues within 4Å: Chain A: R.48, S.49, S.196 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.49, A:S.196, A:S.196, A:S.196 Salt bridges: A:R.48 PO4.3: 4 residues within 4Å: Chain B: R.48, S.49, K.195, S.196 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.49, B:S.196, B:S.196 Water bridges: B:S.53, B:D.194 Salt bridges: B:R.48 PO4.5: 5 residues within 4Å: Chain C: R.48, S.49, K.195, S.196 Chain D: R.105 7 PLIP interactions: 1 interactions with chain D, 6 interactions with chain C Salt bridges: D:R.105, C:R.48 Hydrogen bonds: C:S.49, C:S.196, C:S.196 Water bridges: C:R.48, C:S.50 PO4.7: 2 residues within 4Å: Chain D: R.48, S.49 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.49 Water bridges: D:R.48, D:S.50, D:S.53, D:D.232 Salt bridges: D:R.48

4 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.2: 12 residues within 4Å: Chain A: N.10, K.40, S.42, K.45, Q.98, P.100, A.101, K.123, R.153, H.184, F.219, E.221 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.42, A:A.101 Water bridges: A:N.47, A:F.102, A:R.153 Salt bridges: A:K.40, A:K.45, A:K.123, A:K.123, A:R.153, A:H.184, A:H.184 PEP.4: 12 residues within 4Å: Chain B: N.10, K.40, S.42, K.45, Q.98, P.100, A.101, K.123, R.153, H.184, F.219, E.221 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:N.10, B:S.42, B:A.101, B:E.221 Water bridges: B:R.153, B:R.153 Salt bridges: B:K.40, B:K.45, B:K.123, B:K.123, B:R.153, B:H.184, B:H.184 PEP.6: 13 residues within 4Å: Chain C: N.10, K.40, S.42, K.45, D.80, Q.98, P.100, A.101, K.123, R.153, H.184, F.219, E.221 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:S.42, C:A.101 Water bridges: C:K.45, C:N.47, C:Q.126, C:R.153 Salt bridges: C:K.40, C:K.45, C:K.123, C:K.123, C:R.153, C:H.184, C:H.184 PEP.8: 13 residues within 4Å: Chain D: N.10, K.40, S.42, K.45, D.80, Q.98, P.100, A.101, K.123, R.153, H.184, F.219, E.221 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:S.42, D:A.101 Water bridges: D:N.10, D:N.47, D:N.47, D:D.80, D:F.102 Salt bridges: D:K.40, D:K.45, D:K.123, D:K.123, D:R.153, D:H.184, D:H.184

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
E

B
F

C
G

D
H

2-dehydro-3-deoxyphosphooctonate aldolase

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