SMTL ID : 2nxg.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

2 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.1: 14 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 Ligands: A5P.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.42, A:A.101 Water bridges: A:F.102, A:R.153, A:R.153 Salt bridges: A:K.40, A:K.45, A:K.123, A:K.123, A:R.153, A:H.184 PEP.4: 14 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 Ligands: A5P.5 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:S.42, C:A.101 Water bridges: C:F.102, C:R.153, C:R.153 Salt bridges: C:K.40, C:K.45, C:K.123, C:K.123, C:R.153, C:H.184

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

A5P.2: 12 residues within 4Å: Chain A: N.10, K.45, N.47, R.48, S.49, H.184, Q.187, K.195, S.196, D.232 Chain B: R.105 Ligands: PEP.1 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.10, A:K.45, A:K.45, A:N.47, A:S.49, A:S.49, A:Q.187, A:S.196, A:S.196, A:D.232 Water bridges: A:S.50, A:Q.126, A:R.153, B:R.105 Salt bridges: A:R.48, B:R.105 A5P.5: 12 residues within 4Å: Chain C: N.10, K.45, N.47, R.48, S.49, H.184, Q.187, K.195, S.196, D.232 Chain D: R.105 Ligands: PEP.4 16 PLIP interactions: 14 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:N.10, C:K.45, C:K.45, C:N.47, C:S.49, C:S.49, C:Q.187, C:S.196, C:S.196, C:D.232 Water bridges: C:S.50, C:Q.126, C:R.153, D:R.105 Salt bridges: C:R.48, D:R.105

2 x 1NT: (2R,4R,5R,6R,7R)-2,4,5,6,7-PENTAHYDROXY-2,8-BIS(PHOSPHONOOXY)OCTANOIC ACID(Non-covalent)

1NT.3: 19 residues within 4Å: Chain A: R.105 Chain B: N.10, K.40, S.42, K.45, N.47, R.48, S.49, D.80, Q.98, P.100, A.101, K.123, R.153, H.184, Q.187, F.219, E.221, D.232 29 PLIP interactions: 27 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.10, B:S.42, B:K.45, B:N.47, B:N.47, B:S.49, B:S.49, B:S.49, B:A.101, B:K.123, B:R.153, B:H.184, B:Q.187, B:D.232 Water bridges: B:S.42, B:K.45, B:N.47, B:N.47, B:F.102, B:Q.126, A:R.105 Salt bridges: B:K.40, B:K.45, B:R.48, B:K.123, B:K.123, B:R.153, B:H.184, A:R.105 1NT.6: 19 residues within 4Å: Chain C: R.105 Chain D: N.10, K.40, S.42, K.45, N.47, R.48, S.49, D.80, Q.98, P.100, A.101, K.123, R.153, H.184, Q.187, F.219, E.221, D.232 30 PLIP interactions: 28 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:N.10, D:S.42, D:K.45, D:N.47, D:N.47, D:S.49, D:S.49, D:S.49, D:A.101, D:K.123, D:R.153, D:H.184, D:Q.187, D:D.232 Water bridges: D:S.42, D:K.45, D:N.47, D:N.47, D:D.80, D:F.102, D:Q.126, C:R.105 Salt bridges: D:K.40, D:K.45, D:R.48, D:K.123, D:K.123, D:R.153, D:H.184, C:R.105

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

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