SMTL ID : 2nxi.3 (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 2.30 Å

Oligo State

homo-tetramer

Ligands

5 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.1: 13 residues within 4Å: Chain A: 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 A Hydrogen bonds: A:S.42, A:Q.98, A:A.101 Water bridges: A:N.10, A:N.47, A:N.47, A:F.102 Salt bridges: A:K.40, A:K.45, A:K.123, A:K.123, A:R.153, A:H.184, A:H.184 PEP.2: 8 residues within 4Å: Chain A: N.47, R.48, S.49, Q.187, K.195, S.196, D.232 Chain B: R.105 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.49, A:S.49, A:Q.187, B:R.105 Water bridges: A:N.47, A:S.53 Salt bridges: A:R.48, B:R.105 PEP.4: 13 residues within 4Å: Chain B: 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 B Hydrogen bonds: B:S.42, B:Q.98, B:A.101 Water bridges: B:N.47, B:N.47, B:F.102 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, N.47, D.80, Q.98, P.100, A.101, K.123, R.153, H.184, E.221 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:S.42, C:N.47, C:Q.98, C:A.101 Water bridges: C:F.102 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 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:S.42, D:Q.98, D:A.101 Salt bridges: D:K.40, D:K.45, D:K.123, D:K.123, D:R.153, D:H.184, D:H.184

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

PO4.3: 6 residues within 4Å: Chain A: R.105 Chain B: R.48, S.49, K.195, S.196, D.232 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.49, B:S.196 Water bridges: B:R.48, B:S.196 Salt bridges: B:R.48 PO4.5: 3 residues within 4Å: Chain C: R.48, S.49, D.232 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.49, C:S.49 Salt bridges: C:R.48 PO4.7: 4 residues within 4Å: Chain C: R.105 Chain D: R.48, S.49, D.232 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.49, D:S.49, C:R.105 Water bridges: D:G.190 Salt bridges: D:R.48

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

2007-07-24

Peptides

2-dehydro-3-deoxyphosphooctonate aldolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

B
J

C
K

D
L

2-dehydro-3-deoxyphosphooctonate aldolase

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