SMTL ID : 3c6c.1

Crystal structure of a putative 3-keto-5-aminohexanoate cleavage enzyme (reut_c6226) from ralstonia eutropha jmp134 at 1.72 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-tetramer

Ligands

4 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 3 residues within 4Å: Chain A: H.66, H.68, E.269 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.66, A:H.68, A:E.269, H2O.2, H2O.2, H2O.6 NI.7: 3 residues within 4Å: Chain B: H.66, H.68, E.269 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.66, B:H.68, B:E.269, H2O.17, H2O.17, H2O.21 NI.13: 3 residues within 4Å: Chain C: H.66, H.68, E.269 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:H.66, C:H.68, C:E.269, H2O.32, H2O.32, H2O.36 NI.19: 3 residues within 4Å: Chain D: H.66, H.68, E.269 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:H.66, D:H.68, D:E.269, H2O.47, H2O.48, H2O.51

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 5 residues within 4Å: Chain A: V.217, I.246, R.265, E.269, D.270 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.217, A:I.246 Hydrogen bonds: A:D.270 Water bridges: A:R.265 Salt bridges: A:R.265 ACT.8: 5 residues within 4Å: Chain B: V.217, I.246, R.265, E.269, D.270 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.217, B:I.246 Hydrogen bonds: B:D.270 Water bridges: B:R.265 Salt bridges: B:R.265 ACT.14: 5 residues within 4Å: Chain C: V.217, I.246, R.265, E.269, D.270 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.217, C:I.246 Water bridges: C:R.265 Salt bridges: C:R.265 ACT.20: 5 residues within 4Å: Chain D: V.217, I.246, R.265, E.269, D.270 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:V.217, D:I.246 Water bridges: D:R.265 Salt bridges: D:R.265

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 1 residues within 4Å: Chain A: F.36 2 PLIP interactions: 2 interactions with chain A Water bridges: A:P.41, A:Q.49 EDO.4: 6 residues within 4Å: Chain A: L.140, P.141, E.142, L.179, G.180, I.181 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.179 EDO.5: 4 residues within 4Å: Chain A: P.41, S.42, F.279, T.281 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.42 EDO.9: 1 residues within 4Å: Chain B: F.36 2 PLIP interactions: 2 interactions with chain B Water bridges: B:P.41, B:Q.49 EDO.10: 6 residues within 4Å: Chain B: L.140, P.141, E.142, L.179, G.180, I.181 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.179 EDO.11: 4 residues within 4Å: Chain B: P.41, S.42, F.279, T.281 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.42 EDO.15: 1 residues within 4Å: Chain C: F.36 2 PLIP interactions: 2 interactions with chain C Water bridges: C:P.41, C:Q.49 EDO.16: 6 residues within 4Å: Chain C: L.140, P.141, E.142, L.179, G.180, I.181 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.179 EDO.17: 4 residues within 4Å: Chain C: P.41, S.42, F.279, T.281 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.42 EDO.21: 1 residues within 4Å: Chain D: F.36 2 PLIP interactions: 2 interactions with chain D Water bridges: D:P.41, D:Q.49 EDO.22: 6 residues within 4Å: Chain D: L.140, P.141, E.142, L.179, G.180, I.181 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.179 EDO.23: 4 residues within 4Å: Chain D: P.41, S.42, F.279, T.281 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.42

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 10 residues within 4Å: Chain A: T.31, A.34, M.43, I.246, G.247, L.268, E.269, D.270, N.271, L.272 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.247, A:L.268 PEG.12: 10 residues within 4Å: Chain B: T.31, A.34, M.43, I.246, G.247, L.268, E.269, D.270, N.271, L.272 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.247, B:L.268 PEG.18: 10 residues within 4Å: Chain C: T.31, A.34, M.43, I.246, G.247, L.268, E.269, D.270, N.271, L.272 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.247, C:L.268 PEG.24: 10 residues within 4Å: Chain D: T.31, A.34, M.43, I.246, G.247, L.268, E.269, D.270, N.271, L.272 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.247, D:L.268

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of 3-keto-5-aminohexanoate cleavage enzyme (YP_293392.1) from Ralstonia eutropha JMP134 at 1.72 A resolution. To be published

Release Date

2008-02-19

Peptides

3-keto-5-aminohexanoate cleavage enzyme: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

3-keto-5-aminohexanoate cleavage enzyme