SMTL ID : 2v5h.1

Controlling the storage of nitrogen as arginine: the complex of PII and acetylglutamate kinase from Synechococcus elongatus PCC 7942

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

hetero-6-6-mer

Ligands

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

NLG.1: 13 residues within 4Å: Chain A: G.89, G.90, G.91, I.94, L.111, R.112, L.126, V.169, S.194, N.205, I.206, N.207, A.208 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.126, A:V.169, A:A.208 Hydrogen bonds: A:G.90, A:G.91, A:R.112, A:N.205, A:I.206, A:A.208 Salt bridges: A:R.112 NLG.3: 12 residues within 4Å: Chain B: G.89, G.90, G.91, I.94, L.111, R.112, V.169, S.194, N.205, I.206, N.207, A.208 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.169 Hydrogen bonds: B:G.90, B:G.91, B:R.112, B:N.205, B:N.205, B:A.208 Salt bridges: B:K.55, B:R.112 NLG.5: 11 residues within 4Å: Chain C: G.89, G.90, G.91, I.94, R.112, L.126, S.194, N.205, I.206, N.207, A.208 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:L.126, C:A.208 Hydrogen bonds: C:G.90, C:G.91, C:R.112, C:N.205, C:I.206, C:A.208 Salt bridges: C:K.55, C:R.112 NLG.7: 11 residues within 4Å: Chain D: G.89, G.90, G.91, I.94, L.111, R.112, V.169, N.205, I.206, N.207, A.208 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:V.169 Hydrogen bonds: D:G.90, D:R.112, D:N.205, D:N.205, D:A.208 Salt bridges: D:K.55, D:R.112 NLG.9: 11 residues within 4Å: Chain E: G.89, G.90, G.91, I.94, L.111, R.112, V.169, N.205, I.206, N.207, A.208 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:V.169 Hydrogen bonds: E:G.90, E:G.91, E:R.112, E:N.205, E:N.205, E:A.208 Salt bridges: E:K.55, E:R.112 NLG.12: 11 residues within 4Å: Chain F: G.89, G.90, G.91, I.94, L.111, R.112, V.169, N.205, I.206, N.207, A.208 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:V.169 Hydrogen bonds: F:G.90, F:R.112, F:N.205, F:N.205, F:A.208 Water bridges: F:K.55, F:N.207 Salt bridges: F:K.55, F:R.112

6 x NA: SODIUM ION(Non-functional Binders)

NA.2: 2 residues within 4Å: Chain A: E.297, T.300 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.297 NA.4: 2 residues within 4Å: Chain B: E.297, T.300 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.302 NA.6: 2 residues within 4Å: Chain C: E.297, T.300 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.297 NA.8: 2 residues within 4Å: Chain D: E.297, T.300 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.297 NA.11: 2 residues within 4Å: Chain E: E.297, T.300 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.300 NA.13: 2 residues within 4Å: Chain F: E.297, T.300 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:T.300

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 5 residues within 4Å: Chain D: G.201 Chain E: K.132, D.133, S.136, R.137 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:D.133, E:D.133, E:S.136, D:S.203

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.14: 6 residues within 4Å: Chain G: Q.39, I.86, G.87, D.88 Chain I: R.101, R.103 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain G: R.103 Chain H: I.86, G.87, D.88 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain H: R.101, R.103 Chain I: I.86, G.87, D.88 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain J: R.101, R.103 Chain K: I.86, G.87 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain J: I.86, G.87 Chain L: R.103 Ligand excluded by PLIP CL.19: 5 residues within 4Å: Chain K: R.101, R.103 Chain L: I.86, G.87, D.88 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Llacer, J.L. et al., The Crystal Structure of the Complex of Pii and Acetylglutamate Kinase Reveals How Pii Controls the Storage of Nitrogen as Arginine. Proc.Natl.Acad.Sci.USA (2007)

Release Date

2007-10-16

Peptides

ACETYLGLUTAMATE KINASE: ABCDEF
NITROGEN REGULATORY PROTEIN P-II: GHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

ACETYLGLUTAMATE KINASE

NITROGEN REGULATORY PROTEIN P-II

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