SMTL ID : 2nwr.1

Crystal structure of C11N mutant of KDO8P Synthase in complex with PEP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

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

PO4.1: 3 residues within 4Å: Chain A: R.49, S.50 Chain B: R.106 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.50 Water bridges: A:R.49, A:S.50, A:S.50, A:S.51, A:S.54, A:Q.188, B:R.106 Salt bridges: A:R.49, B:R.106 PO4.3: 3 residues within 4Å: Chain A: R.106 Chain B: R.49, S.50 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.50 Water bridges: B:R.49, B:S.50, B:S.51, B:G.191, B:D.233, A:R.106, A:R.106, A:R.106 Salt bridges: B:R.49, A:R.106 PO4.5: 3 residues within 4Å: Chain C: R.49, S.50 Chain D: R.106 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:S.50 Water bridges: C:S.50, C:S.50, C:S.51, C:S.54, C:Q.188, C:D.233, D:R.106 Salt bridges: C:R.49, D:R.106 PO4.7: 3 residues within 4Å: Chain C: R.106 Chain D: R.49, S.50 11 PLIP interactions: 7 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:S.50 Water bridges: D:R.49, D:R.49, D:S.50, D:S.51, D:G.191, C:R.106, C:R.106, C:R.106 Salt bridges: D:R.49, C:R.106

4 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.2: 13 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 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.43, A:A.102 Water bridges: A:N.11, A:N.48, A:F.103, 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.4: 13 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 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.43, B:A.102 Water bridges: B:N.11, B:N.48, B:N.48, B:F.103, 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.6: 13 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 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:S.43, C:A.102 Water bridges: C:N.11, C:N.48, C:D.81, C:F.103, 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.8: 13 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 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:S.43, D:A.102 Water bridges: D:N.11, D:N.48, D:N.48, D:D.81, D:F.103, 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

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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