SMTL ID : 1mly.1

Crystal Structure of 7,8-Diaminopelargonic Acid Synthase in complex with the cis isomer of amiclenomycin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-dimer

Ligands

2 x ACZ: CIS-AMICLENOMYCIN(Non-covalent)

ACZ.1: 7 residues within 4Å: Chain A: W.52, W.53, Y.144, K.274, R.391, F.393 Ligands: PLP.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.53, A:W.53, A:Y.144, A:F.393 Hydrogen bonds: A:K.274 Water bridges: A:R.391 Salt bridges: A:R.391 ACZ.4: 9 residues within 4Å: Chain A: G.307, T.309 Chain B: W.52, Y.144, A.217, R.391, F.393, Y.398 Ligands: PLP.6 9 PLIP interactions: 1 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:T.309 Hydrophobic interactions: B:Y.144, B:A.217 Water bridges: B:Y.144, B:R.391, B:R.391, B:R.391, B:R.391 Salt bridges: B:R.391

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 4 residues within 4Å: Chain A: V.96, T.99, P.100, L.103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.100 NA.5: 4 residues within 4Å: Chain B: V.96, T.99, P.100, L.103 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.99, B:T.99, B:T.99, B:L.103

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.3: 15 residues within 4Å: Chain A: W.53, S.111, G.112, S.113, Y.144, H.145, G.146, E.211, D.245, I.247, A.248, K.274 Chain B: P.308, T.309 Ligands: ACZ.1 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.144, A:E.211, A:A.248 Hydrogen bonds: A:G.112, A:S.113, A:S.113, B:T.309, B:T.309, B:T.309 Water bridges: A:S.111, A:Y.144, A:D.147, A:D.147, A:K.274, A:T.282, A:T.282 pi-Stacking: A:Y.144 PLP.6: 14 residues within 4Å: Chain A: P.308, T.309 Chain B: S.111, G.112, S.113, Y.144, H.145, G.146, E.211, D.245, I.247, A.248, K.274 Ligands: ACZ.4 13 PLIP interactions: 3 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:T.309, A:T.309, B:G.112, B:S.113, B:S.113 Water bridges: A:F.310, B:S.111, B:D.147, B:D.147, B:T.282 Hydrophobic interactions: B:E.211, B:I.247 pi-Stacking: B:Y.144

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sandmark, J. et al., Structural basis for the inhibition of the biosynthesis of biotin by the antibiotic amiclenomycin. J.Biol.Chem. (2002)

Release Date

2002-12-04

Peptides

7,8-diamino-pelargonic acid aminotransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

7,8-diamino-pelargonic acid aminotransferase

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