SMTL ID : 6rts.1

Piperideine-6-carboxylate dehydrogenase from Streptomyces clavuligerus complexed with NAD+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 26 residues within 4Å: Chain A: I.160, S.161, A.162, F.163, N.164, K.187, P.188, S.189, E.190, A.223, A.224, G.227, E.228, T.242, G.243, S.244, M.247, A.250, E.265, L.266, G.267, G.268, C.299, E.399, F.401, F.468 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:T.242 Hydrogen bonds: A:S.161, A:F.163, A:K.187, A:E.190, A:S.244, A:S.244, A:E.265, A:L.266, A:G.268, A:E.399 Water bridges: A:T.245, A:R.303 NAD.11: 27 residues within 4Å: Chain B: I.160, S.161, A.162, F.163, N.164, K.187, P.188, S.189, E.190, A.223, A.224, G.227, E.228, T.242, G.243, S.244, M.247, A.250, V.251, E.265, L.266, G.267, G.268, C.299, E.399, F.401, F.468 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:T.242 Hydrogen bonds: B:S.161, B:F.163, B:K.187, B:E.190, B:S.244, B:S.244, B:E.265, B:L.266, B:G.268, B:E.399 Water bridges: B:T.245, B:M.247, B:R.303, B:E.399 NAD.19: 26 residues within 4Å: Chain C: I.160, S.161, A.162, F.163, N.164, K.187, P.188, S.189, E.190, A.223, A.224, G.227, E.228, T.242, G.243, S.244, M.247, A.250, E.265, L.266, G.267, G.268, C.299, E.399, F.401, F.468 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:T.242 Hydrogen bonds: C:S.161, C:F.163, C:K.187, C:E.190, C:S.244, C:S.244, C:L.266, C:G.268, C:E.399 Water bridges: C:T.245, C:R.303 NAD.29: 27 residues within 4Å: Chain D: I.160, S.161, A.162, F.163, N.164, K.187, P.188, S.189, E.190, A.223, A.224, G.227, E.228, T.242, G.243, S.244, M.247, A.250, V.251, E.265, L.266, G.267, G.268, C.299, E.399, F.401, F.468 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:T.242 Hydrogen bonds: D:S.161, D:F.163, D:K.187, D:E.190, D:S.244, D:S.244, D:L.266, D:G.268, D:E.399 Water bridges: D:T.245, D:M.247, D:R.303

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

SO4.2: 3 residues within 4Å: Chain A: D.412, L.413, R.441 Ligand excluded by PLIP SO4.3: 3 residues within 4Å: Chain A: T.393, A.394, R.397 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: E.369, Q.371, R.383 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: R.501, T.503, L.504 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: R.142 Chain B: S.460 Ligands: ACT.17 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain B: D.412, L.413, R.441 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain B: Q.392, T.393, A.394, R.397 Ligand excluded by PLIP SO4.14: 2 residues within 4Å: Chain B: Q.371, R.383 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain C: D.412, L.413, R.441 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain C: T.393, A.394, R.397 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain C: E.369, Q.371, R.383 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain C: R.501, T.503, L.504 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain C: R.142 Chain D: S.460 Ligands: ACT.35 Ligand excluded by PLIP SO4.30: 3 residues within 4Å: Chain D: D.412, L.413, R.441 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain D: Q.392, T.393, A.394, R.397 Ligand excluded by PLIP SO4.32: 2 residues within 4Å: Chain D: Q.371, R.383 Ligand excluded by PLIP

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: R.38, G.43, N.343, E.344, A.345 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.38, A:G.43, A:E.344, A:A.345 Water bridges: A:E.344, A:E.344 GOL.8: 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.9: 5 residues within 4Å: Chain A: S.277, A.434, D.435 Chain D: A.434, D.435 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:S.277, A:S.277, D:D.435 GOL.15: 4 residues within 4Å: Chain A: L.154, R.490 Chain B: E.471, K.472 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.16: 7 residues within 4Å: Chain B: E.118, W.172, A.462, E.463, I.464, F.468, S.480 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.118, B:G.466, B:S.480 Water bridges: B:I.464 GOL.25: 5 residues within 4Å: Chain C: R.38, G.43, N.343, E.344, A.345 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.38, C:G.43, C:E.344, C:A.345 GOL.26: 4 residues within 4Å: Chain C: E.471, K.472 Chain D: L.154, R.490 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:L.154, C:E.471, C:K.472 Water bridges: D:F.259, C:K.472 GOL.27: 5 residues within 4Å: Chain B: A.434, D.435 Chain C: S.277, A.434, D.435 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.277, C:S.277, C:D.435 GOL.33: 4 residues within 4Å: Chain C: L.154, R.490 Chain D: E.471, K.472 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 GOL.34: 7 residues within 4Å: Chain D: E.118, W.172, A.462, E.463, I.464, F.468, S.480 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.118, D:G.466, D:S.480 Water bridges: D:I.464

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

ACT.10: 6 residues within 4Å: Chain A: F.165, W.172, R.298, C.299, T.300, F.468 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.300 Hydrogen bonds: A:C.299, A:T.300, A:T.300 ACT.17: 4 residues within 4Å: Chain B: F.289, R.298, S.460 Ligands: SO4.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.289 Water bridges: B:A.290 Salt bridges: B:R.298 ACT.18: 3 residues within 4Å: Chain B: M.389, P.390, T.409 No protein-ligand interaction detected (PLIP) ACT.28: 6 residues within 4Å: Chain C: F.165, W.172, R.298, C.299, T.300, F.468 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:T.300 Hydrogen bonds: C:C.299, C:T.300, C:T.300 ACT.35: 4 residues within 4Å: Chain D: F.289, R.298, S.460 Ligands: SO4.24 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:F.289 Water bridges: D:A.290 Salt bridges: D:R.298 ACT.36: 3 residues within 4Å: Chain D: M.389, P.390, T.409 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.409

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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