SMTL ID : 6rtt.1

Piperideine-6-carboxylate dehydrogenase from Streptomyces clavuligerus complexed with picolinic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-tetramer

Ligands

10 x 6PC: PYRIDINE-2-CARBOXYLIC ACID(Non-covalent)

6PC.1: 8 residues within 4Å: Chain A: E.118, F.165, V.169, W.172, R.298, C.299, T.300, F.468 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.165, A:V.169, A:W.172, A:F.468 Hydrogen bonds: A:C.299, A:T.300 Water bridges: A:T.300, A:T.300 pi-Stacking: A:F.165 6PC.2: 7 residues within 4Å: Chain A: A.162, N.164, G.243, S.244, C.299, E.399, F.401 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.162 pi-Stacking: A:F.401 6PC.3: 5 residues within 4Å: Chain A: P.424, K.472, E.473 Chain B: R.258 Ligands: GOL.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.473 Water bridges: A:K.472 Salt bridges: A:K.472 6PC.9: 7 residues within 4Å: Chain B: F.165, V.169, W.172, R.298, C.299, T.300, F.468 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.165, B:V.169, B:W.172, B:F.468 Hydrogen bonds: B:C.299, B:T.300 Water bridges: B:T.300, B:T.300 pi-Stacking: B:F.165 6PC.10: 6 residues within 4Å: Chain A: R.258, F.259 Chain B: P.424, K.472, E.473 Ligands: GOL.14 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:E.473, A:F.259 Salt bridges: B:K.472 6PC.15: 8 residues within 4Å: Chain C: E.118, F.165, V.169, W.172, R.298, C.299, T.300, F.468 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.165, C:V.169, C:W.172, C:F.468 Hydrogen bonds: C:C.299, C:T.300 pi-Stacking: C:F.165 6PC.16: 7 residues within 4Å: Chain C: A.162, N.164, G.243, S.244, C.299, E.399, F.401 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.162 pi-Stacking: C:F.401 6PC.17: 5 residues within 4Å: Chain C: P.424, K.472, E.473 Chain D: R.258 Ligands: GOL.22 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:E.473 Water bridges: C:K.472 Salt bridges: C:K.472 6PC.23: 7 residues within 4Å: Chain D: F.165, V.169, W.172, R.298, C.299, T.300, F.468 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:F.165, D:V.169, D:W.172, D:F.468 Hydrogen bonds: D:C.299, D:T.300 pi-Stacking: D:F.165 6PC.24: 6 residues within 4Å: Chain C: R.258, F.259 Chain D: P.424, K.472, E.473 Ligands: GOL.28 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.259, D:E.473 Salt bridges: D:K.472

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

SO4.4: 3 residues within 4Å: Chain A: D.412, L.413, R.441 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:L.413 Water bridges: A:D.412, A:D.412, A:E.438, A:R.441, A:R.441, A:R.441, A:R.441, A:R.441 Salt bridges: A:R.441 SO4.5: 3 residues within 4Å: Chain A: T.393, A.394, R.397 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.394 Salt bridges: A:R.397 SO4.6: 2 residues within 4Å: Chain A: Q.371, R.383 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.371 Salt bridges: A:R.383 SO4.7: 2 residues within 4Å: Chain A: T.503, L.504 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.504 Water bridges: A:G.507 SO4.11: 3 residues within 4Å: Chain B: D.412, L.413, R.441 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:L.413 Water bridges: B:E.438, B:R.441, B:R.441, B:R.441, B:R.441, B:R.441 Salt bridges: B:R.441 SO4.12: 3 residues within 4Å: Chain B: T.393, A.394, R.397 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.394 Salt bridges: B:R.397 SO4.13: 2 residues within 4Å: Chain B: Q.371, R.383 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.371 Water bridges: B:G.367, B:R.383, B:R.383 Salt bridges: B:R.383 SO4.18: 3 residues within 4Å: Chain C: D.412, L.413, R.441 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:D.412, C:L.413 Water bridges: C:D.412, C:D.412, C:E.438, C:R.441, C:R.441, C:R.441, C:R.441, C:R.441 Salt bridges: C:R.441 SO4.19: 3 residues within 4Å: Chain C: T.393, A.394, R.397 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.394 Salt bridges: C:R.397 SO4.20: 2 residues within 4Å: Chain C: Q.371, R.383 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.371 Salt bridges: C:R.383 SO4.21: 2 residues within 4Å: Chain C: T.503, L.504 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.504 Water bridges: C:G.507 SO4.25: 3 residues within 4Å: Chain D: D.412, L.413, R.441 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:D.412, D:L.413 Water bridges: D:R.441, D:R.441, D:R.441, D:R.441, D:R.441, D:R.441 Salt bridges: D:R.441 SO4.26: 3 residues within 4Å: Chain D: T.393, A.394, R.397 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.394 Salt bridges: D:R.397 SO4.27: 2 residues within 4Å: Chain D: Q.371, R.383 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.371 Water bridges: D:G.367, D:R.383, D:R.383 Salt bridges: D:R.383

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 5 residues within 4Å: Chain A: E.471, K.472 Chain B: L.154, R.490 Ligands: 6PC.3 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:L.154, A:E.471, A:E.471, A:K.472 Water bridges: B:F.259, A:K.472 GOL.14: 5 residues within 4Å: Chain A: L.154, R.490 Chain B: E.471, K.472 Ligands: 6PC.10 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.471, B:E.471, B:K.472, A:L.154 Water bridges: B:K.472, A:F.259 GOL.22: 5 residues within 4Å: Chain C: E.471, K.472 Chain D: L.154, R.490 Ligands: 6PC.17 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.28: 5 residues within 4Å: Chain C: L.154, R.490 Chain D: E.471, K.472 Ligands: 6PC.24 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:L.154, D:E.471, D:K.472 Water bridges: C:F.259, D:K.472

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

Related Entries With Identical Sequence