SMTL ID : 1zha.1

A. aeolicus KDO8PS R106G mutant in complex with PEP and R5P

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-tetramer

Ligands

2 x R5P: RIBOSE-5-PHOSPHATE(Non-covalent)

R5P.1: 8 residues within 4Å: Chain A: N.48, R.49, S.50, R.154, H.185, Q.188, D.233 Ligands: PEP.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:N.48, A:S.50, A:S.50, A:R.154, A:Q.188 Water bridges: A:K.46, A:K.46, A:N.48, A:N.48, A:S.54, A:A.102, A:Q.127, A:Q.127, A:G.191 Salt bridges: A:R.49 R5P.7: 8 residues within 4Å: Chain C: N.48, R.49, S.50, R.154, H.185, Q.188, D.233 Ligands: PEP.9 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:N.48, C:S.50, C:S.50, C:R.154, C:Q.188 Water bridges: C:K.46, C:K.46, C:N.48, C:N.48, C:S.54, C:A.102, C:Q.127, C:Q.127, C:G.191 Salt bridges: C:R.49

4 x CD: CADMIUM ION(Non-covalent)

CD.2: 4 residues within 4Å: Chain A: C.11, H.185, E.222, D.233 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.11, A:H.185, A:E.222, A:D.233, H2O.5 CD.5: 4 residues within 4Å: Chain B: C.11, H.185, E.222, D.233 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.11, B:H.185, B:E.222, B:D.233, H2O.13 CD.8: 4 residues within 4Å: Chain C: C.11, H.185, E.222, D.233 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.11, C:H.185, C:E.222, C:D.233, H2O.24 CD.11: 4 residues within 4Å: Chain D: C.11, H.185, E.222, D.233 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.11, D:H.185, D:E.222, D:D.233, H2O.32

4 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.3: 13 residues within 4Å: Chain A: 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: R5P.1 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.43, A:A.102 Water bridges: A:K.46, A:N.48, A:F.103, A:Q.127 Salt bridges: A:K.41, A:K.46, A:K.124, A:K.124, A:R.154, A:H.185, A:H.185 PEP.6: 11 residues within 4Å: Chain B: K.41, S.43, K.46, Q.99, P.101, A.102, K.124, R.154, H.185, F.220, E.222 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.43, B:A.102 Water bridges: B:K.46, 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.9: 13 residues within 4Å: Chain C: 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: R5P.7 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:S.43, C:A.102 Water bridges: C:K.46, C:N.48, 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.12: 11 residues within 4Å: Chain D: K.41, S.43, K.46, Q.99, P.101, A.102, K.124, R.154, H.185, F.220, E.222 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:S.43, D:A.102 Water bridges: D:K.46, 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

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

PO4.4: 2 residues within 4Å: Chain B: R.49, S.50 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.50 Water bridges: B:S.50, B:S.50, B:S.51, B:S.54 Salt bridges: B:R.49 PO4.10: 2 residues within 4Å: Chain D: R.49, S.50 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.50 Water bridges: D:S.50, D:S.50, D:S.51, D:S.54 Salt bridges: D:R.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, X. et al., The Catalytic and Conformational Cycle of Aquifex aeolicus KDO8P Synthase: Role of the L7 Loop. Biochemistry (2005)

Release Date

2005-09-27

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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