SMTL ID : 6rtu.1

Piperideine-6-carboxylate dehydrogenase from Streptomyces clavuligerus complexed with alpha-aminoadipic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

2 x UN1: 2-AMINOHEXANEDIOIC ACID(Non-covalent)

UN1.1: 13 residues within 4Å: Chain A: E.118, N.164, F.165, W.172, T.242, E.265, R.298, C.299, T.300, S.460, G.461, A.462, F.468 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.165, A:F.165, A:F.165, A:W.172, A:F.468 Hydrogen bonds: A:E.118, A:N.164, A:C.299, A:T.300, A:T.300, A:G.461, A:A.462 Salt bridges: A:R.298 UN1.18: 13 residues within 4Å: Chain C: E.118, N.164, F.165, W.172, T.242, E.265, R.298, C.299, T.300, S.460, G.461, A.462, F.468 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:F.165, C:F.165, C:F.165, C:W.172, C:F.468 Hydrogen bonds: C:E.118, C:N.164, C:C.299, C:T.300, C:G.461, C:A.462 Salt bridges: C:R.298

20 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: 4 residues within 4Å: Chain A: Q.392, 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: 2 residues within 4Å: Chain A: Q.18, R.22 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: R.501, T.503, L.504 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain B: D.412, L.413, R.441 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain B: T.393, A.394, R.397 Ligand excluded by PLIP SO4.11: 2 residues within 4Å: Chain B: Q.371, R.383 Ligand excluded by PLIP SO4.12: 6 residues within 4Å: Chain B: V.502, L.504, V.508, D.509, F.510, S.511 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain A: G.476, R.478 Chain B: W.151, R.491 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain C: D.412, L.413, R.441 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain C: Q.392, T.393, A.394, R.397 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain C: E.369, Q.371, R.383 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain C: Q.18, R.22 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain C: R.501, T.503, L.504 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain D: D.412, L.413, R.441 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain D: T.393, A.394, R.397 Ligand excluded by PLIP SO4.28: 2 residues within 4Å: Chain D: Q.371, R.383 Ligand excluded by PLIP SO4.29: 6 residues within 4Å: Chain D: V.502, L.504, V.508, D.509, F.510, S.511 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain C: G.476, R.478 Chain D: W.151, R.491 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 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.38, A:R.38, A:E.344, A:A.345 Water bridges: A:N.343, A:E.344, A:E.344, A:E.344 GOL.8: 4 residues within 4Å: Chain A: E.471, K.472 Chain B: L.154, R.490 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Water bridges: B:P.153, B:L.154, B:L.154, B:F.259, A:K.472 Hydrogen bonds: A:E.471, A:E.471, A:K.472 GOL.14: 5 residues within 4Å: Chain B: R.38, G.43, N.343, E.344, A.345 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.38, B:R.38, B:E.344, B:A.345 Water bridges: B:N.343 GOL.15: 4 residues within 4Å: Chain A: L.154, R.490 Chain B: E.471, K.472 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:L.154, B:E.471, B:E.471, B:K.472 Water bridges: A:F.259, B:K.472 GOL.16: 8 residues within 4Å: Chain B: E.118, W.172, A.462, E.463, I.464, G.466, F.468, S.480 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.118, B:G.466, B:S.480 GOL.24: 5 residues within 4Å: Chain C: R.38, G.43, N.343, E.344, A.345 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.38, C:R.38, C:E.344, C:A.345 Water bridges: C:N.343, C:E.344 GOL.25: 4 residues within 4Å: Chain C: E.471, K.472 Chain D: L.154, R.490 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Water bridges: D:P.153, D:L.154, D:L.154, D:F.259, C:K.472 Hydrogen bonds: C:E.471, C:K.472 GOL.31: 5 residues within 4Å: Chain D: R.38, G.43, N.343, E.344, A.345 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.38, D:R.38, D:E.344, D:A.345 Water bridges: D:N.343, D:E.344 GOL.32: 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.33: 8 residues within 4Å: Chain D: E.118, W.172, A.462, E.463, I.464, G.466, F.468, S.480 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.118, D:G.466, D:S.480

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

ACT.17: 3 residues within 4Å: Chain B: R.388, P.390, T.409 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.389 Water bridges: B:R.388, B:T.409 Salt bridges: B:R.388 ACT.34: 3 residues within 4Å: Chain D: R.388, P.390, T.409 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:M.389, D:T.409 Water bridges: D:R.388, D:T.409 Salt bridges: D:R.388

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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