SMTL ID : 1j0a.3 (2 other biounits)

Crystal Structure Analysis of the ACC deaminase homologue

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 8 residues within 4Å: Chain A: K.54, S.81, N.82, H.83, G.157, Y.256, Y.282 Ligands: PLP.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.81, A:N.82, A:H.83, A:Y.256, A:Y.282 Water bridges: A:S.81, A:G.157 Salt bridges: A:K.54 SO4.4: 8 residues within 4Å: Chain B: K.54, S.81, N.82, H.83, G.157, Y.256, Y.282 Ligands: PLP.5 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.81, B:N.82, B:H.83, B:Y.282, B:Y.282 Water bridges: B:S.81, B:G.157, B:Y.256 Salt bridges: B:K.54 SO4.7: 8 residues within 4Å: Chain C: K.54, S.81, N.82, H.83, G.157, Y.256, Y.282 Ligands: PLP.9 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:N.82, C:N.82, C:H.83, C:Y.282, C:Y.282 Water bridges: C:H.80, C:S.81, C:G.157, C:Y.256 Salt bridges: C:K.54 SO4.8: 8 residues within 4Å: Chain D: K.54, S.81, N.82, H.83, G.157, Y.256, Y.282 Ligands: PLP.10 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.81, D:N.82, D:H.83, D:Y.282 Water bridges: D:G.157 Salt bridges: D:K.54 SO4.11: 8 residues within 4Å: Chain E: K.54, S.81, N.82, H.83, G.157, Y.256, Y.282 Ligands: PLP.13 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:N.82, E:N.82, E:H.83, E:Y.256, E:Y.282 Water bridges: E:H.80, E:S.81, E:G.157, E:Y.256 Salt bridges: E:K.54 SO4.12: 8 residues within 4Å: Chain F: K.54, S.81, N.82, H.83, G.157, Y.256, Y.282 Ligands: PLP.14 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:S.81, F:N.82, F:H.83, F:Y.256, F:Y.282, F:Y.282 Water bridges: F:G.157 Salt bridges: F:K.54

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

PLP.2: 16 residues within 4Å: Chain A: N.53, K.54, K.57, N.82, A.188, A.189, G.190, S.191, G.192, G.193, T.194, Y.282, T.308, G.309, G.310 Ligands: SO4.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:K.54, A:Y.282 Hydrogen bonds: A:N.53, A:N.82, A:G.190, A:S.191, A:G.192, A:G.193, A:T.194, A:T.194, A:T.194, A:T.308 Salt bridges: A:K.54, A:K.57 pi-Stacking: A:Y.282 PLP.5: 16 residues within 4Å: Chain B: N.53, K.54, K.57, N.82, A.188, A.189, G.190, S.191, G.192, G.193, T.194, Y.282, T.308, G.309, G.310 Ligands: SO4.4 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:K.54, B:Y.282 Hydrogen bonds: B:N.53, B:K.54, B:N.82, B:G.190, B:S.191, B:G.192, B:G.193, B:T.194, B:T.194, B:T.194, B:T.308 Salt bridges: B:K.54, B:K.57 pi-Stacking: B:Y.282 PLP.9: 16 residues within 4Å: Chain C: N.53, K.54, K.57, N.82, A.189, G.190, S.191, G.192, G.193, T.194, D.279, Y.282, T.308, G.309, G.310 Ligands: SO4.7 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:K.54 Hydrogen bonds: C:N.53, C:N.82, C:G.190, C:S.191, C:G.192, C:G.193, C:T.194, C:T.194 Water bridges: C:L.195 Salt bridges: C:K.54, C:K.57 pi-Stacking: C:Y.282 PLP.10: 16 residues within 4Å: Chain D: N.53, K.54, K.57, N.82, A.188, A.189, G.190, S.191, G.192, G.193, T.194, Y.282, T.308, G.309, G.310 Ligands: SO4.8 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:K.54, D:Y.282, D:Y.282 Hydrogen bonds: D:N.53, D:N.82, D:G.190, D:S.191, D:G.192, D:G.193, D:T.194, D:T.194, D:T.194, D:T.308 Water bridges: D:N.53, D:L.195, D:G.310 Salt bridges: D:K.54, D:K.57 pi-Stacking: D:Y.282 PLP.13: 16 residues within 4Å: Chain E: N.53, K.54, K.57, N.82, A.189, G.190, S.191, G.192, G.193, T.194, D.279, Y.282, T.308, G.309, G.310 Ligands: SO4.11 16 PLIP interactions: 16 interactions with chain E Hydrophobic interactions: E:K.54 Hydrogen bonds: E:N.53, E:K.54, E:N.82, E:G.190, E:S.191, E:G.192, E:G.193, E:T.194, E:T.194, E:T.194, E:T.308 Water bridges: E:L.195 Salt bridges: E:K.54, E:K.57 pi-Stacking: E:Y.282 PLP.14: 16 residues within 4Å: Chain F: N.53, K.54, K.57, N.82, A.188, A.189, G.190, S.191, G.192, G.193, T.194, Y.282, T.308, G.309, G.310 Ligands: SO4.12 19 PLIP interactions: 19 interactions with chain F Hydrophobic interactions: F:K.54, F:Y.282, F:Y.282 Hydrogen bonds: F:N.53, F:K.54, F:N.82, F:G.190, F:S.191, F:G.192, F:G.193, F:T.194, F:T.194, F:T.194 Water bridges: F:N.53, F:L.195, F:G.310 Salt bridges: F:K.54, F:K.57 pi-Stacking: F:Y.282

2 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.3: 4 residues within 4Å: Chain A: F.12, R.14, E.16 Chain F: R.14 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain F Hydrophobic interactions: A:R.14, F:R.14 Hydrogen bonds: A:R.14, F:R.14 IPA.6: 4 residues within 4Å: Chain B: F.12, R.14, E.16 Chain D: R.14 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:R.14, D:R.14 Hydrogen bonds: B:R.14, D:R.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fujino, A. et al., Structural and enzymatic properties of 1-aminocyclopropane-1-carboxylate deaminase homologue from Pyrococcus horikoshii. J.Mol.Biol. (2004)

Release Date

2003-05-12

Peptides

1-aminocyclopropane-1-carboxylate deaminase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
B

D
C

E
B

F
C

1-aminocyclopropane-1-carboxylate deaminase

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