SMTL ID : 1zji.1

Aquifex aeolicus KDO8PS R106G mutant in complex with 2PGA and R5P

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-tetramer

Ligands

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

R5P.1: 9 residues within 4Å: Chain A: N.48, R.49, S.50, R.154, H.185, Q.188, D.233 Ligands: CD.2, 2PG.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.48, A:N.48, A:S.50, A:S.50, A:R.154, A:Q.188 Salt bridges: A:R.49 R5P.7: 9 residues within 4Å: Chain C: N.48, R.49, S.50, R.154, H.185, Q.188, D.233 Ligands: CD.8, 2PG.9 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.48, C:N.48, C:S.50, C:S.50, C:R.154, C:Q.188 Salt bridges: C:R.49

4 x CD: CADMIUM ION(Non-covalent)

CD.2: 7 residues within 4Å: Chain A: C.11, K.46, H.185, E.222, D.233 Ligands: R5P.1, 2PG.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.11, A:H.185, A:E.222, A:E.222, A:D.233 CD.5: 5 residues within 4Å: Chain B: C.11, H.185, E.222, D.233 Ligands: 2PG.6 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:C.11, B:H.185, B:E.222, B:E.222, B:D.233 CD.8: 7 residues within 4Å: Chain C: C.11, K.46, H.185, E.222, D.233 Ligands: R5P.7, 2PG.9 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:C.11, C:H.185, C:E.222, C:E.222, C:D.233 CD.11: 5 residues within 4Å: Chain D: C.11, H.185, E.222, D.233 Ligands: 2PG.12 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:C.11, D:H.185, D:E.222, D:E.222, D:D.233

4 x 2PG: 2-PHOSPHOGLYCERIC ACID(Non-covalent)

2PG.3: 14 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, CD.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.43, A:A.102 Water bridges: A:Q.127, 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 2PG.6: 13 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 Ligands: CD.5 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.43, B:A.102 Salt bridges: B:K.41, B:K.46, B:K.124, B:K.124, B:R.154, B:H.185, B:H.185 2PG.9: 14 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, CD.8 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:S.43, C:A.102 Water bridges: C:Q.127, 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 2PG.12: 13 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 Ligands: CD.11 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:S.43, D:A.102 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 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.50 Water bridges: B:S.54, B:S.54 Salt bridges: B:R.49 PO4.10: 2 residues within 4Å: Chain D: R.49, S.50 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.50 Water bridges: D:S.54, 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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