SMTL ID : 3du4.1

Crystal structure of 7-keto-8-aminopelargonic acid bound 7,8-diaminopelargonic acid synthase in bacillus subtilis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 14 residues within 4Å: Chain A: S.112, G.113, A.114, Y.146, H.147, G.148, E.217, D.251, V.253, A.254, K.280 Chain B: H.316, S.317 Ligands: KAP.2 14 PLIP interactions: 8 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:Y.146, A:E.217, A:V.253, A:K.280 Hydrogen bonds: A:G.113, A:A.114, B:S.317, B:S.317 Water bridges: A:E.217, B:H.316, B:S.317, B:S.317 Salt bridges: A:K.280, B:H.316 PLP.3: 14 residues within 4Å: Chain A: H.316, S.317 Chain B: S.112, G.113, A.114, Y.146, H.147, G.148, E.217, D.251, V.253, A.254, K.280 Ligands: KAP.4 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:E.217, B:V.253, B:K.280 Hydrogen bonds: B:G.113, B:A.114, A:S.317, A:S.317 Water bridges: B:Y.146, B:Y.146, B:Y.146, B:E.217 Salt bridges: B:K.280, A:H.316 pi-Stacking: B:Y.146

2 x KAP: 7-KETO-8-AMINOPELARGONIC ACID(Non-covalent)

KAP.2: 12 residues within 4Å: Chain A: F.17, V.53, W.54, Y.146, D.149, F.162, K.280, R.410 Chain B: L.82, G.315, S.317 Ligands: PLP.1 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.54, A:Y.146, A:F.162, A:F.162 Hydrogen bonds: A:K.280, B:G.315 Water bridges: A:R.410 Salt bridges: A:R.410 KAP.4: 12 residues within 4Å: Chain A: L.82, G.315, H.316, S.317 Chain B: F.17, V.53, Y.146, D.149, A.223, K.280, R.410 Ligands: PLP.3 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:L.82, B:V.53, B:Y.146, B:A.223 Hydrogen bonds: A:G.315, B:Y.146 Water bridges: B:R.410 Salt bridges: B:R.410

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dey, S. et al., Structural characterization of the Mycobacterium tuberculosis biotin biosynthesis enzymes 7,8-diaminopelargonic acid synthase and dethiobiotin synthetase . Biochemistry (2010)

Release Date

2009-06-23

Peptides

Adenosylmethionine-8-amino-7-oxononanoate aminotransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Adenosylmethionine-8-amino-7-oxononanoate aminotransferase

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