SMTL ID : 4usj.1

N-acetylglutamate kinase from Arabidopsis thaliana in complex with PII from Chlamydomonas reinhardtii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

hetero-6-6-mer

Ligands

6 x ARG: ARGININE(Non-covalent)

ARG.1: 12 residues within 4Å: Chain A: F.54, K.231, K.253, E.305, I.306, S.308, D.309, E.310, G.311, A.312, G.313, M.315 11 PLIP interactions: 10 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:E.305, A:S.308, A:S.308, A:A.312, A:G.313, A:G.313, A:G.313, A:M.315, R.1 Salt bridges: A:K.231, A:E.305 ARG.5: 11 residues within 4Å: Chain B: F.54, K.231, K.253, E.305, I.306, S.308, D.309, E.310, G.311, G.313, M.315 9 PLIP interactions: 9 interactions with chain B, Hydrogen bonds: B:S.292, B:E.305, B:S.308, B:S.308, B:G.313, B:G.313 Salt bridges: B:K.53, B:K.231, B:E.305 ARG.13: 12 residues within 4Å: Chain E: F.54, K.231, K.253, E.305, I.306, S.308, D.309, E.310, G.311, A.312, G.313, M.315 11 PLIP interactions: 10 interactions with chain E, 1 Ligand-Ligand interactions Hydrogen bonds: E:E.305, E:S.308, E:S.308, E:A.312, E:G.313, E:G.313, E:G.313, E:M.315, R.13 Salt bridges: E:K.231, E:E.305 ARG.17: 11 residues within 4Å: Chain F: F.54, K.231, K.253, E.305, I.306, S.308, D.309, E.310, G.311, G.313, M.315 9 PLIP interactions: 9 interactions with chain F, Hydrogen bonds: F:S.292, F:E.305, F:S.308, F:S.308, F:G.313, F:G.313 Salt bridges: F:K.53, F:K.231, F:E.305 ARG.25: 12 residues within 4Å: Chain I: F.54, K.231, K.253, E.305, I.306, S.308, D.309, E.310, G.311, A.312, G.313, M.315 11 PLIP interactions: 10 interactions with chain I, 1 Ligand-Ligand interactions Hydrogen bonds: I:E.305, I:S.308, I:S.308, I:A.312, I:G.313, I:G.313, I:G.313, I:M.315, R.25 Salt bridges: I:K.231, I:E.305 ARG.29: 11 residues within 4Å: Chain J: F.54, K.231, K.253, E.305, I.306, S.308, D.309, E.310, G.311, G.313, M.315 9 PLIP interactions: 9 interactions with chain J, Hydrogen bonds: J:S.292, J:E.305, J:S.308, J:S.308, J:G.313, J:G.313 Salt bridges: J:K.53, J:K.231, J:E.305

3 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 18 residues within 4Å: Chain A: K.62, G.64, G.65, A.66, T.236, D.237, V.238, G.240, I.241, L.242, K.245, K.268, V.269, A.270, G.272, M.273, K.276 Ligands: MG.4 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:A.66, A:T.236, A:D.237, A:L.242, A:K.268, A:A.270, A:M.273 Water bridges: A:K.62, A:K.62, A:K.62, A:K.62, A:G.65, A:K.276 Salt bridges: A:K.62, A:K.276, A:K.276 ADP.14: 18 residues within 4Å: Chain E: K.62, G.64, G.65, A.66, T.236, D.237, V.238, G.240, I.241, L.242, K.245, K.268, V.269, A.270, G.272, M.273, K.276 Ligands: MG.16 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:A.66, E:T.236, E:D.237, E:L.242, E:K.268, E:A.270, E:M.273 Water bridges: E:K.62, E:K.62, E:K.62, E:K.62, E:G.65, E:K.276 Salt bridges: E:K.62, E:K.276, E:K.276 ADP.26: 18 residues within 4Å: Chain I: K.62, G.64, G.65, A.66, T.236, D.237, V.238, G.240, I.241, L.242, K.245, K.268, V.269, A.270, G.272, M.273, K.276 Ligands: MG.28 16 PLIP interactions: 16 interactions with chain I Hydrogen bonds: I:A.66, I:T.236, I:D.237, I:L.242, I:K.268, I:A.270, I:M.273 Water bridges: I:K.62, I:K.62, I:K.62, I:K.62, I:G.65, I:K.276 Salt bridges: I:K.62, I:K.276, I:K.276

3 x NLG: N-ACETYL-L-GLUTAMATE(Non-covalent)

NLG.3: 13 residues within 4Å: Chain A: G.96, G.97, G.98, I.101, G.117, L.118, R.119, V.177, S.202, N.213, I.214, N.215, A.216 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.177 Hydrogen bonds: A:G.97, A:G.98, A:R.119, A:N.213, A:N.213, A:N.213, A:N.215, A:A.216 Water bridges: A:K.62, A:K.62, A:K.62 Salt bridges: A:K.62, A:R.119 NLG.15: 13 residues within 4Å: Chain E: G.96, G.97, G.98, I.101, G.117, L.118, R.119, V.177, S.202, N.213, I.214, N.215, A.216 14 PLIP interactions: 14 interactions with chain E Hydrophobic interactions: E:V.177 Hydrogen bonds: E:G.97, E:G.98, E:R.119, E:N.213, E:N.213, E:N.213, E:N.215, E:A.216 Water bridges: E:K.62, E:K.62, E:K.62 Salt bridges: E:K.62, E:R.119 NLG.27: 13 residues within 4Å: Chain I: G.96, G.97, G.98, I.101, G.117, L.118, R.119, V.177, S.202, N.213, I.214, N.215, A.216 14 PLIP interactions: 14 interactions with chain I Hydrophobic interactions: I:V.177 Hydrogen bonds: I:G.97, I:G.98, I:R.119, I:N.213, I:N.213, I:N.213, I:N.215, I:A.216 Water bridges: I:K.62, I:K.62, I:K.62 Salt bridges: I:K.62, I:R.119

9 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.4: 1 residues within 4Å: Ligands: ADP.2 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain C: G.54, G.105 Ligands: ATP.7 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:G.54, H2O.3, H2O.3 MG.11: 2 residues within 4Å: Chain D: G.54 Ligands: ATP.10 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:G.54, H2O.4, H2O.4 MG.16: 1 residues within 4Å: Ligands: ADP.14 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain G: G.54, G.105 Ligands: ATP.19 3 PLIP interactions: 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:G.54, H2O.7, H2O.7 MG.23: 2 residues within 4Å: Chain H: G.54 Ligands: ATP.22 3 PLIP interactions: 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:G.54, H2O.8, H2O.8 MG.28: 1 residues within 4Å: Ligands: ADP.26 No protein-ligand interaction detected (PLIP) MG.32: 3 residues within 4Å: Chain K: G.54, G.105 Ligands: ATP.31 3 PLIP interactions: 1 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:G.54, H2O.11, H2O.11 MG.35: 2 residues within 4Å: Chain L: G.54 Ligands: ATP.34 3 PLIP interactions: 1 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:G.54, H2O.12, H2O.12

3 x X2W: N-ACETYL-L-GLUTAMYL 5-PHOSPHATE(Non-covalent)

X2W.6: 14 residues within 4Å: Chain B: K.62, G.65, M.68, G.96, G.97, G.98, P.99, I.101, L.118, R.119, V.177, N.213, N.215, A.216 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.177 Hydrogen bonds: B:G.65, B:G.97, B:G.98, B:R.119, B:N.213, B:N.213, B:N.213, B:A.216 Water bridges: B:N.215 Salt bridges: B:K.62, B:K.62, B:R.119 X2W.18: 14 residues within 4Å: Chain F: K.62, G.65, M.68, G.96, G.97, G.98, P.99, I.101, L.118, R.119, V.177, N.213, N.215, A.216 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:V.177 Hydrogen bonds: F:G.65, F:G.97, F:G.98, F:R.119, F:N.213, F:N.213, F:N.213, F:A.216 Water bridges: F:N.215 Salt bridges: F:K.62, F:K.62, F:R.119 X2W.30: 14 residues within 4Å: Chain J: K.62, G.65, M.68, G.96, G.97, G.98, P.99, I.101, L.118, R.119, V.177, N.213, N.215, A.216 13 PLIP interactions: 13 interactions with chain J Hydrophobic interactions: J:V.177 Hydrogen bonds: J:G.65, J:G.97, J:G.98, J:R.119, J:N.213, J:N.213, J:N.213, J:A.216 Water bridges: J:N.215 Salt bridges: J:K.62, J:K.62, J:R.119

6 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.7: 22 residues within 4Å: Chain C: I.24, G.52, V.53, G.54, Q.56, K.76, I.104, G.105, D.106, G.107, K.108, F.110 Chain G: G.44, L.45, T.46, D.80, V.82, R.119, R.121, M.132 Ligands: MG.8, GLN.21 15 PLIP interactions: 7 interactions with chain C, 8 interactions with chain G Hydrogen bonds: C:V.53, C:Q.56, C:G.105, C:G.107, G:T.46, G:V.82, G:V.82 Water bridges: C:Q.56, G:I.120, G:I.120 Salt bridges: C:K.108, G:R.119, G:R.119, G:R.121 pi-Stacking: C:F.110 ATP.10: 22 residues within 4Å: Chain D: I.24, G.52, V.53, G.54, Q.56, I.104, G.105, D.106, G.107, K.108, F.110 Chain L: G.44, L.45, T.46, D.80, I.81, V.82, R.119, R.121, M.132 Ligands: MG.11, GLN.36 15 PLIP interactions: 9 interactions with chain D, 6 interactions with chain L Hydrogen bonds: D:V.53, D:Q.56, D:G.105, D:G.107, L:V.82, L:V.82 Water bridges: D:G.54, D:Q.56, D:E.61, L:I.120 Salt bridges: D:K.108, L:R.119, L:R.119, L:R.121 pi-Stacking: D:F.110 ATP.19: 22 residues within 4Å: Chain G: I.24, G.52, V.53, G.54, Q.56, K.76, I.104, G.105, D.106, G.107, K.108, F.110 Chain K: G.44, L.45, T.46, D.80, V.82, R.119, R.121, M.132 Ligands: MG.20, GLN.33 14 PLIP interactions: 7 interactions with chain G, 7 interactions with chain K Hydrogen bonds: G:V.53, G:Q.56, G:G.105, G:G.107, K:V.82, K:V.82 Water bridges: G:Q.56, K:I.120, K:I.120 Salt bridges: G:K.108, K:R.119, K:R.119, K:R.121 pi-Stacking: G:F.110 ATP.22: 22 residues within 4Å: Chain D: G.44, L.45, T.46, D.80, I.81, V.82, R.119, R.121, M.132 Chain H: I.24, G.52, V.53, G.54, Q.56, I.104, G.105, D.106, G.107, K.108, F.110 Ligands: GLN.12, MG.23 16 PLIP interactions: 9 interactions with chain H, 7 interactions with chain D Hydrogen bonds: H:V.53, H:Q.56, H:G.105, H:G.107, D:T.46, D:V.82, D:V.82 Water bridges: H:G.54, H:Q.56, H:E.61, D:I.120 Salt bridges: H:K.108, D:R.119, D:R.119, D:R.121 pi-Stacking: H:F.110 ATP.31: 22 residues within 4Å: Chain C: G.44, L.45, T.46, D.80, V.82, R.119, R.121, M.132 Chain K: I.24, G.52, V.53, G.54, Q.56, K.76, I.104, G.105, D.106, G.107, K.108, F.110 Ligands: GLN.9, MG.32 15 PLIP interactions: 7 interactions with chain K, 8 interactions with chain C Hydrogen bonds: K:V.53, K:Q.56, K:G.105, K:G.107, C:T.46, C:V.82, C:V.82 Water bridges: K:Q.56, C:I.120, C:I.120 Salt bridges: K:K.108, C:R.119, C:R.119, C:R.121 pi-Stacking: K:F.110 ATP.34: 22 residues within 4Å: Chain H: G.44, L.45, T.46, D.80, I.81, V.82, R.119, R.121, M.132 Chain L: I.24, G.52, V.53, G.54, Q.56, I.104, G.105, D.106, G.107, K.108, F.110 Ligands: GLN.24, MG.35 16 PLIP interactions: 7 interactions with chain H, 9 interactions with chain L Hydrogen bonds: H:T.46, H:V.82, H:V.82, L:V.53, L:Q.56, L:G.105, L:G.107 Water bridges: H:I.120, L:G.54, L:Q.56, L:E.61 Salt bridges: H:R.119, H:R.119, H:R.121, L:K.108 pi-Stacking: L:F.110

6 x GLN: GLUTAMINE(Non-covalent)

GLN.9: 14 residues within 4Å: Chain C: I.42, R.43, G.44, I.81, V.82, V.83, Q.87, E.130, K.131, M.132, G.135, M.136, E.137 Ligands: ATP.31 8 PLIP interactions: 8 interactions with chain C, Hydrogen bonds: C:R.43, C:G.44, C:V.82, C:Q.87, C:Q.87, C:E.130, C:M.132, C:E.137 GLN.12: 14 residues within 4Å: Chain D: I.42, R.43, G.44, I.81, V.82, V.83, Q.87, E.130, K.131, M.132, G.135, M.136, E.137 Ligands: ATP.22 8 PLIP interactions: 8 interactions with chain D, Hydrogen bonds: D:R.43, D:G.44, D:V.82, D:Q.87, D:Q.87, D:E.130, D:M.132, D:E.137 GLN.21: 14 residues within 4Å: Chain G: I.42, R.43, G.44, I.81, V.82, V.83, Q.87, E.130, K.131, M.132, G.135, M.136, E.137 Ligands: ATP.7 8 PLIP interactions: 8 interactions with chain G, Hydrogen bonds: G:R.43, G:G.44, G:V.82, G:Q.87, G:Q.87, G:E.130, G:M.132, G:E.137 GLN.24: 14 residues within 4Å: Chain H: I.42, R.43, G.44, I.81, V.82, V.83, Q.87, E.130, K.131, M.132, G.135, M.136, E.137 Ligands: ATP.34 8 PLIP interactions: 8 interactions with chain H, Hydrogen bonds: H:R.43, H:G.44, H:V.82, H:Q.87, H:Q.87, H:E.130, H:M.132, H:E.137 GLN.33: 14 residues within 4Å: Chain K: I.42, R.43, G.44, I.81, V.82, V.83, Q.87, E.130, K.131, M.132, G.135, M.136, E.137 Ligands: ATP.19 8 PLIP interactions: 8 interactions with chain K, Hydrogen bonds: K:R.43, K:G.44, K:V.82, K:Q.87, K:Q.87, K:E.130, K:M.132, K:E.137 GLN.36: 14 residues within 4Å: Chain L: I.42, R.43, G.44, I.81, V.82, V.83, Q.87, E.130, K.131, M.132, G.135, M.136, E.137 Ligands: ATP.10 8 PLIP interactions: 8 interactions with chain L, Hydrogen bonds: L:R.43, L:G.44, L:V.82, L:Q.87, L:Q.87, L:E.130, L:M.132, L:E.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chellamuthu, V.R. et al., A Widespread Glutamine-Sensing Mechanism in the Plant Kingdom. Cell(Cambridge,Mass.) (2014)

Release Date

2014-12-03

Peptides

ACETYLGLUTAMATE KINASE, CHLOROPLASTIC: ABEFIJ
NITROGEN REGULATORY PROTEIN PII: CDGHKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
A

F
B

I
A

J
B

C
C

D
D

G
C

H
D

K
C

L
D

ACETYLGLUTAMATE KINASE, CHLOROPLASTIC

NITROGEN REGULATORY PROTEIN PII

Related Entries With Identical Sequence