SMTL ID : 1qj3.1

Crystal structure of 7,8-diaminopelargonic acid synthase in complex with 7-keto-8-aminopelargonic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 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: KAP.2 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:E.211, A:I.247, A:K.274 Hydrogen bonds: A:G.112, A:S.113, A:S.113, B:T.309, B:T.309 Water bridges: A:D.147, A:D.147, A:T.148, A:E.211, B:F.310 Salt bridges: A:K.274 pi-Stacking: A:Y.144 PLP.4: 15 residues within 4Å: Chain A: P.308, T.309 Chain B: W.53, S.111, G.112, S.113, Y.144, H.145, G.146, E.211, D.245, I.247, A.248, K.274 Ligands: KAP.5 16 PLIP interactions: 12 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:E.211, B:I.247, B:K.274 Hydrogen bonds: B:G.112, B:S.113, B:S.113, B:K.274, A:T.309, A:T.309, A:T.309 Water bridges: B:D.147, B:D.147, B:K.274, A:F.310 Salt bridges: B:K.274 pi-Stacking: B:Y.144

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

KAP.2: 10 residues within 4Å: Chain A: Y.17, W.52, Y.144, A.217, K.274, R.391, F.393 Chain B: G.307, T.309 Ligands: PLP.1 10 PLIP interactions: 1 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:G.307, A:Y.17, A:W.52, A:Y.144, A:K.274 Hydrophobic interactions: A:W.52, A:Y.144, A:A.217, A:F.393 Salt bridges: A:R.391 KAP.5: 11 residues within 4Å: Chain A: G.307, T.309 Chain B: Y.17, W.52, W.53, Y.144, A.217, K.274, R.391, F.393 Ligands: PLP.4 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.52, B:W.53, B:F.393, B:F.393 Hydrogen bonds: B:W.52, B:Y.144 Water bridges: B:Y.398 Salt bridges: B:R.391

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

NA.3: 5 residues within 4Å: Chain A: V.96, T.99, P.100, Q.101, L.103 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.99, A:T.99, A:T.99, A:L.103 NA.6: 4 residues within 4Å: Chain B: V.96, T.99, P.100, L.103 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.96, B:T.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kack, H. et al., Crystal Structure of Diaminopelargonic Acid Synthase; Evolutionary Relationships between Pyridoxal-5'-Phosphate Dependent Enzymes. J.Mol.Biol. (1999)

Release Date

2000-06-22

Peptides

7,8-DIAMINOPELARGONIC ACID SYNTHASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

7,8-DIAMINOPELARGONIC ACID SYNTHASE

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