SMTL ID : 1dj9.2 (1 other biounit)

CRYSTAL STRUCTURE OF 8-AMINO-7-OXONANOATE SYNTHASE (OR 7-KETO-8AMINIPELARGONATE OR KAPA SYNTHASE) COMPLEXED WITH PLP AND THE PRODUCT 8(S)-AMINO-7-OXONANONOATE (OR KAPA). THE ENZYME OF BIOTIN BIOSYNTHETIC PATHWAY.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: L.147, R.148, R.149 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.149, A:R.149 Water bridges: A:R.148 Salt bridges: A:R.149 SO4.2: 5 residues within 4Å: Chain A: R.21, R.22, R.23 Chain B: R.101, L.256 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.101, A:R.23 Hydrogen bonds: A:R.23 SO4.5: 3 residues within 4Å: Chain B: L.147, R.148, R.149 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.149, B:R.149 Water bridges: B:R.148 Salt bridges: B:R.149 SO4.6: 5 residues within 4Å: Chain A: R.101, L.256 Chain B: R.21, R.22, R.23 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.23 Salt bridges: B:R.23, A:R.101

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: H.133, S.179, H.207 Ligands: KAM.4 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.179, H2O.3, H2O.4 MG.7: 4 residues within 4Å: Chain B: H.133, S.179, H.207 Ligands: KAM.8 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.179, H2O.16, H2O.17

2 x KAM: N-[7-KETO-8-AMINOPELARGONIC ACID]-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE](Non-covalent)

KAM.4: 25 residues within 4Å: Chain A: R.21, S.107, G.108, F.109, N.112, H.133, E.175, S.179, D.204, A.206, H.207, T.233, K.236, G.242, I.348, R.349, T.352 Chain B: S.76, H.78, V.79, I.263, Y.264, S.265, T.266 Ligands: MG.3 24 PLIP interactions: 18 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:H.133, A:A.206, A:T.352, B:H.78, B:V.79, B:Y.264 Hydrogen bonds: A:S.107, A:G.108, A:F.109, A:K.236, B:T.266, B:T.266 Water bridges: A:N.47, A:N.47, A:S.179, A:K.236, A:G.347, A:R.349, A:R.349, A:R.349, B:T.266 Salt bridges: A:R.21, A:K.236 pi-Stacking: A:H.133 KAM.8: 25 residues within 4Å: Chain A: S.76, H.78, V.79, I.263, Y.264, S.265, T.266 Chain B: R.21, S.107, G.108, F.109, N.112, H.133, E.175, S.179, D.204, A.206, H.207, T.233, K.236, G.242, I.348, R.349, T.352 Ligands: MG.7 26 PLIP interactions: 20 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:H.133, B:A.206, B:T.352, A:H.78, A:V.79, A:Y.264 Hydrogen bonds: B:S.107, B:G.108, B:F.109, B:T.233, B:K.236, B:T.352, A:T.266, A:T.266 Water bridges: B:N.47, B:N.47, B:S.179, B:K.236, B:G.347, B:R.349, B:R.349, B:R.349, A:T.266 Salt bridges: B:R.21, B:K.236 pi-Stacking: B:H.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Webster, S.P. et al., Mechanism of 8-amino-7-oxononanoate synthase: spectroscopic, kinetic, and crystallographic studies. Biochemistry (2000)

Release Date

2000-12-06

Peptides

8-AMINO-7-OXONONANOATE SYNTHASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

8-AMINO-7-OXONONANOATE SYNTHASE

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