SMTL ID : 1nyt.3 (2 other biounits)

SHIKIMATE DEHYDROGENASE AroE COMPLEXED WITH NADP+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-octamer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: R.117, Y.209 Ligand excluded by PLIP SO4.2: 3 residues within 4Å: Chain A: H.205, P.206, G.207 Ligand excluded by PLIP SO4.3: 7 residues within 4Å: Chain A: I.11, S.14, S.16, T.61, Y.215, L.241 Ligands: DTV.6 Ligand excluded by PLIP SO4.4: 5 residues within 4Å: Chain A: E.111, R.112, S.114 Chain B: Q.26, L.27 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain A: N.28 Chain B: S.114, R.117 Chain E: Q.21 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain B: T.61, V.62, K.65 Ligands: NAP.11 Ligand excluded by PLIP SO4.9: 6 residues within 4Å: Chain B: T.61, V.62, P.63, F.64, K.65, E.66 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain B: F.51, S.52, R.90, G.94 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain C: R.117, Y.209 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain C: H.205, P.206, G.207 Ligand excluded by PLIP SO4.14: 7 residues within 4Å: Chain C: I.11, S.14, S.16, T.61, Y.215, L.241 Ligands: DTV.17 Ligand excluded by PLIP SO4.15: 5 residues within 4Å: Chain C: E.111, R.112, S.114 Chain D: Q.26, L.27 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain C: N.28 Chain D: S.114, R.117 Chain G: Q.21 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain D: T.61, V.62, K.65 Ligands: NAP.22 Ligand excluded by PLIP SO4.20: 6 residues within 4Å: Chain D: T.61, V.62, P.63, F.64, K.65, E.66 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain D: F.51, S.52, R.90, G.94 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain E: R.117, L.120, Y.209 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain E: H.205, P.206, G.207 Ligand excluded by PLIP SO4.25: 5 residues within 4Å: Chain E: I.11, S.14, S.16, T.61, L.241 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain E: E.111 Chain F: Q.26 Ligand excluded by PLIP SO4.28: 2 residues within 4Å: Chain F: I.116, R.117 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain F: T.61, V.62, K.65 Ligands: NAP.30 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain G: R.117, L.120, Y.209 Ligand excluded by PLIP SO4.32: 3 residues within 4Å: Chain G: H.205, P.206, G.207 Ligand excluded by PLIP SO4.33: 5 residues within 4Å: Chain G: I.11, S.14, S.16, T.61, L.241 Ligand excluded by PLIP SO4.34: 2 residues within 4Å: Chain G: E.111 Chain H: Q.26 Ligand excluded by PLIP SO4.36: 2 residues within 4Å: Chain H: I.116, R.117 Ligand excluded by PLIP SO4.37: 4 residues within 4Å: Chain H: T.61, V.62, K.65 Ligands: NAP.38 Ligand excluded by PLIP

8 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.5: 24 residues within 4Å: Chain A: V.62, P.63, K.65, D.102, G.126, A.127, G.128, G.129, A.130, N.149, R.150, T.151, R.154, A.187, T.188, S.189, S.190, M.213, Y.215, G.237, M.240, L.241, Q.244 Ligands: DTV.6 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:A.130 Hydrogen bonds: A:A.127, A:G.128, A:G.129, A:A.130, A:N.149, A:R.150, A:R.150, A:T.151, A:T.151, A:T.188, A:S.189, A:M.213, A:L.241 Water bridges: A:S.131, A:R.150, A:R.154, A:R.154, A:R.154, A:R.154, A:S.189, A:S.189, A:D.195, A:D.195, A:D.195, A:D.195, A:I.196 Salt bridges: A:R.150, A:R.154 pi-Cation interactions: A:R.150, A:R.150 NAP.11: 20 residues within 4Å: Chain B: G.126, A.127, G.128, G.129, A.130, N.149, R.150, T.151, R.154, A.187, T.188, S.189, S.190, M.213, F.214, G.237, M.240, L.241, Q.244 Ligands: SO4.8 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:A.130 Hydrogen bonds: B:A.127, B:G.128, B:G.129, B:A.130, B:N.149, B:R.150, B:R.150, B:T.151, B:T.151, B:T.188, B:S.189, B:M.213, B:L.241, B:Q.244 Water bridges: B:S.131, B:R.150, B:R.150, B:S.189 Salt bridges: B:R.150, B:R.154 pi-Cation interactions: B:R.150, B:R.150 NAP.16: 24 residues within 4Å: Chain C: V.62, P.63, K.65, D.102, G.126, A.127, G.128, G.129, A.130, N.149, R.150, T.151, R.154, A.187, T.188, S.189, S.190, M.213, Y.215, G.237, M.240, L.241, Q.244 Ligands: DTV.17 31 PLIP interactions: 31 interactions with chain C Hydrophobic interactions: C:A.130 Hydrogen bonds: C:A.127, C:G.128, C:G.129, C:A.130, C:N.149, C:R.150, C:R.150, C:T.151, C:T.188, C:S.189, C:M.213, C:L.241 Water bridges: C:E.66, C:S.131, C:R.150, C:T.151, C:R.154, C:R.154, C:R.154, C:S.189, C:S.189, C:D.195, C:D.195, C:D.195, C:I.196, C:Y.215 Salt bridges: C:R.150, C:R.154 pi-Cation interactions: C:R.150, C:R.150 NAP.22: 20 residues within 4Å: Chain D: G.126, A.127, G.128, G.129, A.130, N.149, R.150, T.151, R.154, A.187, T.188, S.189, S.190, M.213, F.214, G.237, M.240, L.241, Q.244 Ligands: SO4.19 24 PLIP interactions: 24 interactions with chain D Hydrophobic interactions: D:A.130 Hydrogen bonds: D:A.127, D:G.128, D:G.129, D:A.130, D:N.149, D:R.150, D:R.150, D:T.151, D:T.188, D:S.189, D:M.213, D:L.241, D:Q.244 Water bridges: D:S.131, D:R.150, D:R.150, D:T.151, D:T.151, D:S.189 Salt bridges: D:R.150, D:R.154 pi-Cation interactions: D:R.150, D:R.150 NAP.27: 21 residues within 4Å: Chain E: V.62, P.63, K.65, D.102, G.126, A.127, G.128, G.129, A.130, N.149, R.150, T.151, R.154, A.187, T.188, S.189, S.190, M.213, G.237, M.240, L.241 30 PLIP interactions: 30 interactions with chain E Hydrophobic interactions: E:A.130 Hydrogen bonds: E:A.127, E:G.128, E:G.129, E:A.130, E:N.149, E:R.150, E:R.150, E:T.151, E:T.151, E:T.188, E:S.189, E:M.213 Water bridges: E:V.62, E:S.131, E:R.150, E:R.154, E:R.154, E:R.154, E:R.154, E:S.189, E:S.193, E:S.193, E:D.195, E:D.195, E:I.196 Salt bridges: E:R.150, E:R.154 pi-Cation interactions: E:R.150, E:R.150 NAP.30: 22 residues within 4Å: Chain F: V.62, K.65, D.102, G.126, A.127, G.128, G.129, A.130, N.149, R.150, T.151, R.154, A.187, T.188, S.189, S.190, M.213, Y.215, G.237, M.240, L.241 Ligands: SO4.29 25 PLIP interactions: 25 interactions with chain F Hydrophobic interactions: F:A.130 Hydrogen bonds: F:A.127, F:G.128, F:G.129, F:A.130, F:N.149, F:R.150, F:R.150, F:T.151, F:T.151, F:T.188, F:S.189, F:M.213, F:L.241 Water bridges: F:S.131, F:R.150, F:R.154, F:R.154, F:R.154, F:R.154, F:I.196 Salt bridges: F:R.150, F:R.154 pi-Cation interactions: F:R.150, F:R.150 NAP.35: 21 residues within 4Å: Chain G: V.62, P.63, K.65, D.102, G.126, A.127, G.128, G.129, A.130, N.149, R.150, T.151, R.154, A.187, T.188, S.189, S.190, M.213, G.237, M.240, L.241 30 PLIP interactions: 30 interactions with chain G Hydrophobic interactions: G:A.130 Hydrogen bonds: G:A.127, G:G.128, G:G.129, G:A.130, G:N.149, G:R.150, G:R.150, G:T.151, G:T.188, G:S.189, G:M.213 Water bridges: G:V.62, G:E.66, G:S.131, G:R.150, G:T.151, G:T.151, G:R.154, G:R.154, G:S.189, G:S.193, G:S.193, G:D.195, G:D.195, G:I.196 Salt bridges: G:R.150, G:R.154 pi-Cation interactions: G:R.150, G:R.150 NAP.38: 22 residues within 4Å: Chain H: V.62, K.65, D.102, G.126, A.127, G.128, G.129, A.130, N.149, R.150, T.151, R.154, A.187, T.188, S.189, S.190, M.213, Y.215, G.237, M.240, L.241 Ligands: SO4.37 25 PLIP interactions: 25 interactions with chain H Hydrophobic interactions: H:A.130 Hydrogen bonds: H:A.127, H:G.128, H:G.129, H:A.130, H:N.149, H:R.150, H:R.150, H:T.151, H:T.188, H:S.189, H:M.213, H:L.241 Water bridges: H:S.131, H:R.150, H:T.151, H:T.151, H:R.154, H:R.154, H:I.196, H:Y.215 Salt bridges: H:R.150, H:R.154 pi-Cation interactions: H:R.150, H:R.150

2 x DTV: (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL(Non-covalent)

DTV.6: 11 residues within 4Å: Chain A: N.59, V.60, T.61, V.62, K.65, N.86, D.102, L.241, Q.244 Ligands: SO4.3, NAP.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.65, A:N.86 DTV.17: 11 residues within 4Å: Chain C: N.59, V.60, T.61, V.62, K.65, N.86, D.102, L.241, Q.244 Ligands: SO4.14, NAP.16 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.65, C:N.86 Water bridges: C:Y.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Michel, G. et al., Structures of shikimate dehydrogenase AroE and its Paralog YdiB. A common structural framework for different activities. J.Biol.Chem. (2003)

Release Date

2003-03-04

Peptides

Shikimate 5-dehydrogenase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
A

D
C

E
B

F
D

G
B

H
D

Shikimate 5-dehydrogenase

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