SMTL ID : 6rtr.1

Piperideine-6-carboxylate dehydrogenase from Streptomyces clavuligerus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: D.412, L.413, R.441 Ligand excluded by PLIP SO4.2: 3 residues within 4Å: Chain A: T.393, A.394, R.397 Ligand excluded by PLIP SO4.3: 4 residues within 4Å: Chain A: V.2, E.369, Q.371, R.383 Ligand excluded by PLIP SO4.4: 2 residues within 4Å: Chain A: Q.18, R.22 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: R.501, T.503, L.504 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain B: D.412, L.413, R.441 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain B: E.360, T.393, A.394, R.397 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain B: E.369, Q.371, R.383 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain C: D.412, L.413, R.441 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain C: T.393, A.394, R.397 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain C: V.2, E.369, Q.371, R.383 Ligand excluded by PLIP SO4.19: 2 residues within 4Å: Chain C: Q.18, R.22 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain C: R.501, T.503, L.504 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain D: D.412, L.413, R.441 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain D: E.360, T.393, A.394, R.397 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain D: E.369, Q.371, R.383 Ligand excluded by PLIP

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: E.471, K.472 Chain B: L.154, R.490 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.471, A:E.471, A:K.472, B:L.154 Water bridges: A:K.472, B:F.259 GOL.7: 5 residues within 4Å: Chain A: S.277, A.434, D.435 Chain D: A.434, D.435 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:D.435, A:S.277, A:S.277 GOL.9: 2 residues within 4Å: Chain B: V.502, L.504 No protein-ligand interaction detected (PLIP) GOL.13: 5 residues within 4Å: Chain B: A.162, F.163, S.189, E.190, L.191 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.163, B:S.189, B:E.190, B:E.190 GOL.21: 4 residues within 4Å: Chain C: E.471, K.472 Chain D: L.154, R.490 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:E.471, C:K.472, D:L.154 Water bridges: C:K.472, D:F.259 GOL.22: 5 residues within 4Å: Chain B: A.434, D.435 Chain C: S.277, A.434, D.435 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:S.277, C:S.277, C:D.435, B:D.435, B:D.435 GOL.24: 2 residues within 4Å: Chain D: V.502, L.504 No protein-ligand interaction detected (PLIP) GOL.28: 5 residues within 4Å: Chain D: A.162, F.163, S.189, E.190, L.191 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:F.163, D:S.189, D:E.190, D:E.190, D:E.190

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

ACT.8: 4 residues within 4Å: Chain A: R.38, G.43, N.343, E.344 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:N.343 Hydrogen bonds: A:E.344 Water bridges: A:R.38, A:R.38, A:R.38, A:G.43, A:E.344, A:E.344, A:A.345 Salt bridges: A:R.38 ACT.14: 3 residues within 4Å: Chain B: M.389, P.390, T.409 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:T.409 Water bridges: B:R.388, B:T.409 Salt bridges: B:R.388 ACT.15: 5 residues within 4Å: Chain B: F.165, R.298, C.299, T.300, F.468 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.165, B:R.298, B:T.300 Hydrogen bonds: B:T.300, B:T.300 ACT.23: 4 residues within 4Å: Chain C: R.38, G.43, N.343, E.344 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:N.343 Hydrogen bonds: C:E.344 Water bridges: C:R.38, C:R.38, C:R.38, C:G.43, C:A.345, C:Y.380 Salt bridges: C:R.38 ACT.29: 3 residues within 4Å: Chain D: M.389, P.390, T.409 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:T.409 Water bridges: D:R.388, D:T.409 Salt bridges: D:R.388 ACT.30: 5 residues within 4Å: Chain D: F.165, R.298, C.299, T.300, F.468 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.165, D:R.298, D:T.300 Hydrogen bonds: D:T.300

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hasse, D. et al., Structure and mechanism of piperideine-6-carboxylate dehydrogenase from Streptomyces clavuligerus. Acta Crystallogr D Struct Biol (2019)

Release Date

2019-12-18

Peptides

Semialdehyde dehydrogenase Pcd: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Semialdehyde dehydrogenase Pcd

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