SMTL ID : 2eg2.2 (1 other biounit)

The crystal structure of PII protein

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-12-mer

Ligands

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

CL.1: 8 residues within 4Å: Chain A: K.3, I.94 Chain E: K.3, I.94 Chain I: K.3, I.94 Ligands: CL.9, CL.17 Ligand excluded by PLIP CL.3: 8 residues within 4Å: Chain B: K.3, I.94 Chain G: K.3, I.94 Chain L: K.3, I.94 Ligands: CL.13, CL.23 Ligand excluded by PLIP CL.5: 8 residues within 4Å: Chain C: K.3, I.94 Chain H: K.3, I.94 Chain J: K.3, I.94 Ligands: CL.15, CL.19 Ligand excluded by PLIP CL.7: 8 residues within 4Å: Chain D: K.3, I.94 Chain F: K.3, I.94 Chain K: K.3, I.94 Ligands: CL.11, CL.21 Ligand excluded by PLIP CL.9: 8 residues within 4Å: Chain A: K.3, I.94 Chain E: K.3, I.94 Chain I: K.3, I.94 Ligands: CL.1, CL.17 Ligand excluded by PLIP CL.11: 8 residues within 4Å: Chain D: K.3, I.94 Chain F: K.3, I.94 Chain K: K.3, I.94 Ligands: CL.7, CL.21 Ligand excluded by PLIP CL.13: 8 residues within 4Å: Chain B: K.3, I.94 Chain G: K.3, I.94 Chain L: K.3, I.94 Ligands: CL.3, CL.23 Ligand excluded by PLIP CL.15: 8 residues within 4Å: Chain C: K.3, I.94 Chain H: K.3, I.94 Chain J: K.3, I.94 Ligands: CL.5, CL.19 Ligand excluded by PLIP CL.17: 8 residues within 4Å: Chain A: K.3, I.94 Chain E: K.3, I.94 Chain I: K.3, I.94 Ligands: CL.1, CL.9 Ligand excluded by PLIP CL.19: 8 residues within 4Å: Chain C: K.3, I.94 Chain H: K.3, I.94 Chain J: K.3, I.94 Ligands: CL.5, CL.15 Ligand excluded by PLIP CL.21: 8 residues within 4Å: Chain D: K.3, I.94 Chain F: K.3, I.94 Chain K: K.3, I.94 Ligands: CL.7, CL.11 Ligand excluded by PLIP CL.23: 8 residues within 4Å: Chain B: K.3, I.94 Chain G: K.3, I.94 Chain L: K.3, I.94 Ligands: CL.3, CL.13 Ligand excluded by PLIP

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

ATP.2: 19 residues within 4Å: Chain A: I.7, G.35, F.36, K.58, R.85, V.86, G.87, D.88, G.89, K.90, F.92 Chain I: G.27, M.28, T.29, E.62, V.63, V.64, R.101, R.103 20 PLIP interactions: 10 interactions with chain A, 10 interactions with chain I Hydrogen bonds: A:F.36, A:G.87, A:D.88, A:G.89, A:K.90, I:M.28, I:T.29, I:V.64, I:V.64 Water bridges: A:K.58, A:K.58, I:G.26, I:I.102, I:R.103 Salt bridges: A:K.58, A:K.90, I:R.101, I:R.101, I:R.103 pi-Stacking: A:F.92 ATP.4: 19 residues within 4Å: Chain B: I.7, G.35, F.36, K.58, R.85, V.86, G.87, D.88, G.89, K.90, F.92 Chain L: G.27, M.28, T.29, E.62, V.63, V.64, R.101, R.103 20 PLIP interactions: 10 interactions with chain B, 10 interactions with chain L Hydrogen bonds: B:F.36, B:G.87, B:D.88, B:G.89, B:K.90, L:M.28, L:T.29, L:V.64, L:V.64 Water bridges: B:K.58, B:K.58, L:G.26, L:I.102, L:R.103 Salt bridges: B:K.58, B:K.90, L:R.101, L:R.101, L:R.103 pi-Stacking: B:F.92 ATP.6: 19 residues within 4Å: Chain C: I.7, G.35, F.36, K.58, R.85, V.86, G.87, D.88, G.89, K.90, F.92 Chain J: G.27, M.28, T.29, E.62, V.63, V.64, R.101, R.103 19 PLIP interactions: 10 interactions with chain C, 9 interactions with chain J Hydrogen bonds: C:F.36, C:G.87, C:D.88, C:G.89, C:K.90, J:M.28, J:V.64, J:V.64 Water bridges: C:K.58, C:K.58, J:G.26, J:I.102, J:R.103 Salt bridges: C:K.58, C:K.90, J:R.101, J:R.101, J:R.103 pi-Stacking: C:F.92 ATP.8: 19 residues within 4Å: Chain D: I.7, G.35, F.36, K.58, R.85, V.86, G.87, D.88, G.89, K.90, F.92 Chain K: G.27, M.28, T.29, E.62, V.63, V.64, R.101, R.103 19 PLIP interactions: 10 interactions with chain D, 9 interactions with chain K Hydrogen bonds: D:F.36, D:G.87, D:D.88, D:G.89, D:K.90, K:M.28, K:V.64, K:V.64 Water bridges: D:K.58, D:K.58, K:G.26, K:I.102, K:R.103 Salt bridges: D:K.58, D:K.90, K:R.101, K:R.101, K:R.103 pi-Stacking: D:F.92 ATP.10: 19 residues within 4Å: Chain A: G.27, M.28, T.29, E.62, V.63, V.64, R.101, R.103 Chain E: I.7, G.35, F.36, K.58, R.85, V.86, G.87, D.88, G.89, K.90, F.92 20 PLIP interactions: 10 interactions with chain E, 10 interactions with chain A Hydrogen bonds: E:F.36, E:G.87, E:D.88, E:G.89, E:K.90, A:M.28, A:T.29, A:V.64, A:V.64 Water bridges: E:K.58, E:K.58, A:G.26, A:I.102, A:R.103 Salt bridges: E:K.58, E:K.90, A:R.101, A:R.101, A:R.103 pi-Stacking: E:F.92 ATP.12: 19 residues within 4Å: Chain D: G.27, M.28, T.29, E.62, V.63, V.64, R.101, R.103 Chain F: I.7, G.35, F.36, K.58, R.85, V.86, G.87, D.88, G.89, K.90, F.92 19 PLIP interactions: 9 interactions with chain D, 10 interactions with chain F Hydrogen bonds: D:M.28, D:V.64, D:V.64, F:F.36, F:G.87, F:D.88, F:G.89, F:K.90 Water bridges: D:G.26, D:I.102, D:R.103, F:K.58, F:K.58 Salt bridges: D:R.101, D:R.101, D:R.103, F:K.58, F:K.90 pi-Stacking: F:F.92 ATP.14: 19 residues within 4Å: Chain B: G.27, M.28, T.29, E.62, V.63, V.64, R.101, R.103 Chain G: I.7, G.35, F.36, K.58, R.85, V.86, G.87, D.88, G.89, K.90, F.92 20 PLIP interactions: 10 interactions with chain B, 10 interactions with chain G Hydrogen bonds: B:M.28, B:T.29, B:V.64, B:V.64, G:F.36, G:G.87, G:D.88, G:G.89, G:K.90 Water bridges: B:G.26, B:I.102, B:R.103, G:K.58, G:K.58 Salt bridges: B:R.101, B:R.101, B:R.103, G:K.58, G:K.90 pi-Stacking: G:F.92 ATP.16: 19 residues within 4Å: Chain C: G.27, M.28, T.29, E.62, V.63, V.64, R.101, R.103 Chain H: I.7, G.35, F.36, K.58, R.85, V.86, G.87, D.88, G.89, K.90, F.92 19 PLIP interactions: 10 interactions with chain H, 9 interactions with chain C Hydrogen bonds: H:F.36, H:G.87, H:D.88, H:G.89, H:K.90, C:M.28, C:V.64, C:V.64 Water bridges: H:K.58, H:K.58, C:G.26, C:I.102, C:R.103 Salt bridges: H:K.58, H:K.90, C:R.101, C:R.101, C:R.103 pi-Stacking: H:F.92 ATP.18: 19 residues within 4Å: Chain E: G.27, M.28, T.29, E.62, V.63, V.64, R.101, R.103 Chain I: I.7, G.35, F.36, K.58, R.85, V.86, G.87, D.88, G.89, K.90, F.92 19 PLIP interactions: 9 interactions with chain E, 10 interactions with chain I Hydrogen bonds: E:M.28, E:V.64, E:V.64, I:F.36, I:G.87, I:D.88, I:G.89, I:K.90 Water bridges: E:G.26, E:I.102, E:R.103, I:K.58, I:K.58 Salt bridges: E:R.101, E:R.101, E:R.103, I:K.58, I:K.90 pi-Stacking: I:F.92 ATP.20: 19 residues within 4Å: Chain H: G.27, M.28, T.29, E.62, V.63, V.64, R.101, R.103 Chain J: I.7, G.35, F.36, K.58, R.85, V.86, G.87, D.88, G.89, K.90, F.92 20 PLIP interactions: 10 interactions with chain J, 10 interactions with chain H Hydrogen bonds: J:F.36, J:G.87, J:D.88, J:G.89, J:K.90, H:M.28, H:T.29, H:V.64, H:V.64 Water bridges: J:K.58, J:K.58, H:G.26, H:I.102, H:R.103 Salt bridges: J:K.58, J:K.90, H:R.101, H:R.101, H:R.103 pi-Stacking: J:F.92 ATP.22: 19 residues within 4Å: Chain F: G.27, M.28, T.29, E.62, V.63, V.64, R.101, R.103 Chain K: I.7, G.35, F.36, K.58, R.85, V.86, G.87, D.88, G.89, K.90, F.92 20 PLIP interactions: 10 interactions with chain F, 10 interactions with chain K Hydrogen bonds: F:M.28, F:T.29, F:V.64, F:V.64, K:F.36, K:G.87, K:D.88, K:G.89, K:K.90 Water bridges: F:G.26, F:I.102, F:R.103, K:K.58, K:K.58 Salt bridges: F:R.101, F:R.101, F:R.103, K:K.58, K:K.90 pi-Stacking: K:F.92 ATP.24: 19 residues within 4Å: Chain G: G.27, M.28, T.29, E.62, V.63, V.64, R.101, R.103 Chain L: I.7, G.35, F.36, K.58, R.85, V.86, G.87, D.88, G.89, K.90, F.92 19 PLIP interactions: 9 interactions with chain G, 10 interactions with chain L Hydrogen bonds: G:M.28, G:V.64, G:V.64, L:F.36, L:G.87, L:D.88, L:G.89, L:K.90 Water bridges: G:G.26, G:I.102, G:R.103, L:K.58, L:K.58 Salt bridges: G:R.101, G:R.101, G:R.103, L:K.58, L:K.90 pi-Stacking: L:F.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sakai, H. et al., The crystal structure of PII protein. To be Published

Release Date

2008-03-04

Peptides

Nitrogen regulatory protein P-II: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

L
A

Nitrogen regulatory protein P-II

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