SMTL ID : 1t8x.1

r106g kdo8ps with pep and a5p

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x CD: CADMIUM ION(Non-covalent)

CD.1: 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.1 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.10 CD.7: 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.17 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.27

4 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.2: 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: A5P.3 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:N.48, 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: 12 residues within 4Å: Chain B: K.41, S.43, K.46, D.81, Q.99, P.101, A.102, K.124, R.154, H.185, F.220, E.222 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.43, B:A.102 Water bridges: B:K.46 Salt bridges: B:K.41, B:K.46, B:K.124, B:K.124, B:R.154, B:H.185, B:H.185 PEP.8: 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: A5P.9 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:N.48, C:Q.127 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: 12 residues within 4Å: Chain D: K.41, S.43, K.46, D.81, 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:D.81 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 A5P: ARABINOSE-5-PHOSPHATE(Non-covalent)

A5P.3: 8 residues within 4Å: Chain A: N.48, R.49, S.50, R.154, H.185, Q.188, D.233 Ligands: PEP.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.48, A:S.50, A:R.154, A:Q.188, A:Q.188 Water bridges: A:N.48, A:N.48, A:Q.127, A:Q.127 Salt bridges: A:R.49 A5P.9: 8 residues within 4Å: Chain C: N.48, R.49, S.50, R.154, H.185, Q.188, D.233 Ligands: PEP.8 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:N.48, C:S.50, C:R.154, C:Q.188, C:Q.188 Water bridges: C:N.48, C:N.48, C:Q.127, C:Q.127 Salt bridges: C:R.49

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

PO4.4: 2 residues within 4Å: Chain B: R.49, S.50 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.50 Water bridges: B:R.49, B:R.49, B:R.49, B:S.50, B:S.51 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:R.49, D:R.49, D:S.50, D:S.51 Salt bridges: D:R.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, X. et al., Effects of the Arg106==>Gly mutation on the catalytic and conformational cycle of Aquifex aeolicus KDO8P synthase. To be Published

Release Date

2005-06-14

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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