SMTL ID : 1tzj.1

Crystal Structure of 1-aminocyclopropane-1-carboxylate deaminase complexed with d-vinyl glycine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-tetramer

Ligands

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

PLP.1: 18 residues within 4Å: Chain A: N.50, K.51, K.54, N.79, S.163, C.196, S.197, V.198, T.199, G.200, S.201, T.202, Y.294, E.295, L.322, G.323, G.324 Ligands: A3B.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:K.51, A:Y.294 Hydrogen bonds: A:N.50, A:N.79, A:V.198, A:T.199, A:G.200, A:S.201, A:T.202, A:T.202 Water bridges: A:N.50, A:Q.203 Salt bridges: A:K.51, A:K.54 pi-Stacking: A:Y.294 PLP.4: 18 residues within 4Å: Chain B: N.50, K.51, K.54, N.79, S.163, C.196, S.197, V.198, T.199, G.200, S.201, T.202, Y.294, E.295, L.322, G.323, G.324 Ligands: SO4.3 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:K.51, B:Y.294 Hydrogen bonds: B:N.50, B:N.79, B:S.163, B:V.198, B:T.199, B:G.200, B:S.201, B:T.202, B:T.202 Water bridges: B:N.50, B:Q.203 Salt bridges: B:K.51, B:K.54 pi-Stacking: B:Y.294 PLP.5: 18 residues within 4Å: Chain C: N.50, K.51, K.54, N.79, S.163, C.196, S.197, V.198, T.199, G.200, S.201, T.202, Y.294, E.295, L.322, G.323, G.324 Ligands: A3B.6 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:K.51, C:Y.294 Hydrogen bonds: C:N.50, C:K.51, C:N.79, C:S.163, C:V.198, C:T.199, C:T.199, C:G.200, C:S.201, C:T.202, C:T.202 Water bridges: C:N.50, C:K.51, C:Q.203 Salt bridges: C:K.51, C:K.54 pi-Stacking: C:Y.294 PLP.8: 18 residues within 4Å: Chain D: N.50, K.51, K.54, N.79, S.163, C.196, S.197, V.198, T.199, G.200, S.201, T.202, Y.294, E.295, L.322, G.323, G.324 Ligands: SO4.7 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:K.51, D:Y.294 Hydrogen bonds: D:N.50, D:K.51, D:N.79, D:S.163, D:V.198, D:T.199, D:T.199, D:G.200, D:T.202, D:T.202 Water bridges: D:N.50, D:Q.203 Salt bridges: D:K.51, D:K.54 pi-Stacking: D:Y.294

2 x A3B: D-VINYLGLYCINE(Non-covalent)

A3B.2: 11 residues within 4Å: Chain A: K.51, I.73, G.74, S.78, N.79, Q.80, A.160, G.161, Y.268, Y.294 Ligands: PLP.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Q.80, A:A.160 Hydrogen bonds: A:K.51, A:N.79, A:Q.80, A:Y.268, A:Y.294 Water bridges: A:Y.268 Salt bridges: A:K.51 A3B.6: 10 residues within 4Å: Chain C: K.51, G.74, G.75, S.78, N.79, Q.80, W.102, G.161, Y.294 Ligands: PLP.5 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:W.102 Hydrogen bonds: C:K.51, C:N.79, C:N.79, C:Q.80, C:Y.294 Water bridges: C:S.78, C:Y.294 Salt bridges: C:K.51

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

SO4.3: 7 residues within 4Å: Chain B: K.51, S.78, N.79, Q.80, Y.268, Y.294 Ligands: PLP.4 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.78, B:N.79, B:N.79, B:Q.80 Water bridges: B:S.78, B:G.161 Salt bridges: B:K.51 SO4.7: 7 residues within 4Å: Chain D: K.51, S.78, N.79, Q.80, Y.268, Y.294 Ligands: PLP.8 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:S.78, D:N.79, D:Q.80, D:Y.268, D:Y.294 Water bridges: D:S.78, D:G.161 Salt bridges: D:K.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Karthikeyan, S. et al., Structural Analysis of Pseudomonas 1-Aminocyclopropane-1-carboxylate Deaminase Complexes: Insight into the Mechanism of a Unique Pyridoxal-5'-phosphate Dependent Cyclopropane Ring-Opening Reaction. Biochemistry (2004)

Release Date

2004-11-02

Peptides

1-aminocyclopropane-1-carboxylate deaminase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

1-aminocyclopropane-1-carboxylate deaminase

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