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

Crystal structure of Mg(2+) and BeF(3)(-)-bound CheY in complex with CheZ(200-214) solved from a F432 crystal grown in CAPS (pH 10.5)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-12-mer

Ligands

12 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: D.12, D.13, F.14, D.57, N.59 Ligands: BEF.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.13, A:D.57, A:N.59, H2O.3, H2O.3 MG.6: 6 residues within 4Å: Chain B: D.12, D.13, F.14, D.57, N.59 Ligands: BEF.10 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.13, B:D.57, B:N.59, H2O.6, H2O.6 MG.11: 6 residues within 4Å: Chain C: D.12, D.13, F.14, D.57, N.59 Ligands: BEF.15 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.13, C:D.57, C:N.59, H2O.9, H2O.9 MG.16: 6 residues within 4Å: Chain D: D.12, D.13, F.14, D.57, N.59 Ligands: BEF.20 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.13, D:D.57, D:N.59, H2O.12, H2O.12 MG.21: 6 residues within 4Å: Chain E: D.12, D.13, F.14, D.57, N.59 Ligands: BEF.25 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.13, E:D.57, E:N.59, H2O.15, H2O.15 MG.26: 6 residues within 4Å: Chain F: D.12, D.13, F.14, D.57, N.59 Ligands: BEF.30 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.13, F:D.57, F:N.59, H2O.18, H2O.18 MG.31: 6 residues within 4Å: Chain G: D.12, D.13, F.14, D.57, N.59 Ligands: BEF.35 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.13, G:D.57, G:N.59, H2O.21, H2O.21 MG.36: 6 residues within 4Å: Chain H: D.12, D.13, F.14, D.57, N.59 Ligands: BEF.40 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:D.13, H:D.57, H:N.59, H2O.24, H2O.24 MG.41: 6 residues within 4Å: Chain I: D.12, D.13, F.14, D.57, N.59 Ligands: BEF.45 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:D.13, I:D.57, I:N.59, H2O.27, H2O.27 MG.46: 6 residues within 4Å: Chain J: D.12, D.13, F.14, D.57, N.59 Ligands: BEF.50 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:D.13, J:D.57, J:N.59, H2O.30, H2O.31 MG.51: 6 residues within 4Å: Chain K: D.12, D.13, F.14, D.57, N.59 Ligands: BEF.55 5 PLIP interactions: 3 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:D.13, K:D.57, K:N.59, H2O.34, H2O.34 MG.56: 6 residues within 4Å: Chain L: D.12, D.13, F.14, D.57, N.59 Ligands: BEF.60 5 PLIP interactions: 3 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:D.13, L:D.57, L:N.59, H2O.37, H2O.37

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

SO4.2: 5 residues within 4Å: Chain A: K.70 Chain I: K.70 Chain K: K.70 Ligands: SO4.42, SO4.52 3 PLIP interactions: 1 interactions with chain I, 1 interactions with chain A, 1 interactions with chain K Salt bridges: I:K.70, A:K.70, K:K.70 SO4.7: 5 residues within 4Å: Chain B: K.70 Chain F: K.70 Chain J: K.70 Ligands: SO4.27, SO4.47 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain F, 1 interactions with chain J Salt bridges: B:K.70, F:K.70, J:K.70 SO4.12: 5 residues within 4Å: Chain C: K.70 Chain E: K.70 Chain G: K.70 Ligands: SO4.22, SO4.32 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain G, 1 interactions with chain E Salt bridges: C:K.70, G:K.70, E:K.70 SO4.17: 5 residues within 4Å: Chain D: K.70 Chain H: K.70 Chain L: K.70 Ligands: SO4.37, SO4.57 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain L, 1 interactions with chain H Salt bridges: D:K.70, L:K.70, H:K.70 SO4.22: 5 residues within 4Å: Chain C: K.70 Chain E: K.70 Chain G: K.70 Ligands: SO4.12, SO4.32 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain G, 1 interactions with chain E Salt bridges: C:K.70, G:K.70, E:K.70 SO4.27: 5 residues within 4Å: Chain B: K.70 Chain F: K.70 Chain J: K.70 Ligands: SO4.7, SO4.47 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain J, 1 interactions with chain F Salt bridges: B:K.70, J:K.70, F:K.70 SO4.32: 5 residues within 4Å: Chain C: K.70 Chain E: K.70 Chain G: K.70 Ligands: SO4.12, SO4.22 3 PLIP interactions: 1 interactions with chain G, 1 interactions with chain C, 1 interactions with chain E Salt bridges: G:K.70, C:K.70, E:K.70 SO4.37: 5 residues within 4Å: Chain D: K.70 Chain H: K.70 Chain L: K.70 Ligands: SO4.17, SO4.57 3 PLIP interactions: 1 interactions with chain L, 1 interactions with chain H, 1 interactions with chain D Salt bridges: L:K.70, H:K.70, D:K.70 SO4.42: 5 residues within 4Å: Chain A: K.70 Chain I: K.70 Chain K: K.70 Ligands: SO4.2, SO4.52 3 PLIP interactions: 1 interactions with chain K, 1 interactions with chain A, 1 interactions with chain I Salt bridges: K:K.70, A:K.70, I:K.70 SO4.47: 5 residues within 4Å: Chain B: K.70 Chain F: K.70 Chain J: K.70 Ligands: SO4.7, SO4.27 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain J, 1 interactions with chain F Salt bridges: B:K.70, J:K.70, F:K.70 SO4.52: 5 residues within 4Å: Chain A: K.70 Chain I: K.70 Chain K: K.70 Ligands: SO4.2, SO4.42 3 PLIP interactions: 1 interactions with chain I, 1 interactions with chain K, 1 interactions with chain A Salt bridges: I:K.70, K:K.70, A:K.70 SO4.57: 5 residues within 4Å: Chain D: K.70 Chain H: K.70 Chain L: K.70 Ligands: SO4.17, SO4.37 3 PLIP interactions: 1 interactions with chain L, 1 interactions with chain D, 1 interactions with chain H Salt bridges: L:K.70, D:K.70, H:K.70

24 x CXS: 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID(Non-covalent)

CXS.3: 11 residues within 4Å: Chain A: R.73, G.102, A.103, S.104, K.126, L.127 Chain K: T.71, A.74, D.75, S.76, M.78 Ligand excluded by PLIP CXS.4: 6 residues within 4Å: Chain A: E.27, L.28, A.113, E.117, N.121 Chain G: N.31 Ligand excluded by PLIP CXS.8: 11 residues within 4Å: Chain B: R.73, G.102, A.103, S.104, K.126, L.127 Chain F: T.71, A.74, D.75, S.76, M.78 Ligand excluded by PLIP CXS.9: 6 residues within 4Å: Chain B: E.27, L.28, A.113, E.117, N.121 Chain K: N.31 Ligand excluded by PLIP CXS.13: 11 residues within 4Å: Chain C: R.73, G.102, A.103, S.104, K.126, L.127 Chain G: T.71, A.74, D.75, S.76, M.78 Ligand excluded by PLIP CXS.14: 6 residues within 4Å: Chain C: E.27, L.28, A.113, E.117, N.121 Chain F: N.31 Ligand excluded by PLIP CXS.18: 11 residues within 4Å: Chain D: R.73, G.102, A.103, S.104, K.126, L.127 Chain H: T.71, A.74, D.75, S.76, M.78 Ligand excluded by PLIP CXS.19: 6 residues within 4Å: Chain D: E.27, L.28, A.113, E.117, N.121 Chain J: N.31 Ligand excluded by PLIP CXS.23: 11 residues within 4Å: Chain C: T.71, A.74, D.75, S.76, M.78 Chain E: R.73, G.102, A.103, S.104, K.126, L.127 Ligand excluded by PLIP CXS.24: 6 residues within 4Å: Chain E: E.27, L.28, A.113, E.117, N.121 Chain H: N.31 Ligand excluded by PLIP CXS.28: 11 residues within 4Å: Chain F: R.73, G.102, A.103, S.104, K.126, L.127 Chain J: T.71, A.74, D.75, S.76, M.78 Ligand excluded by PLIP CXS.29: 6 residues within 4Å: Chain C: N.31 Chain F: E.27, L.28, A.113, E.117, N.121 Ligand excluded by PLIP CXS.33: 11 residues within 4Å: Chain E: T.71, A.74, D.75, S.76, M.78 Chain G: R.73, G.102, A.103, S.104, K.126, L.127 Ligand excluded by PLIP CXS.34: 6 residues within 4Å: Chain A: N.31 Chain G: E.27, L.28, A.113, E.117, N.121 Ligand excluded by PLIP CXS.38: 11 residues within 4Å: Chain H: R.73, G.102, A.103, S.104, K.126, L.127 Chain L: T.71, A.74, D.75, S.76, M.78 Ligand excluded by PLIP CXS.39: 6 residues within 4Å: Chain E: N.31 Chain H: E.27, L.28, A.113, E.117, N.121 Ligand excluded by PLIP CXS.43: 11 residues within 4Å: Chain A: T.71, A.74, D.75, S.76, M.78 Chain I: R.73, G.102, A.103, S.104, K.126, L.127 Ligand excluded by PLIP CXS.44: 6 residues within 4Å: Chain I: E.27, L.28, A.113, E.117, N.121 Chain L: N.31 Ligand excluded by PLIP CXS.48: 11 residues within 4Å: Chain B: T.71, A.74, D.75, S.76, M.78 Chain J: R.73, G.102, A.103, S.104, K.126, L.127 Ligand excluded by PLIP CXS.49: 6 residues within 4Å: Chain D: N.31 Chain J: E.27, L.28, A.113, E.117, N.121 Ligand excluded by PLIP CXS.53: 11 residues within 4Å: Chain I: T.71, A.74, D.75, S.76, M.78 Chain K: R.73, G.102, A.103, S.104, K.126, L.127 Ligand excluded by PLIP CXS.54: 6 residues within 4Å: Chain B: N.31 Chain K: E.27, L.28, A.113, E.117, N.121 Ligand excluded by PLIP CXS.58: 11 residues within 4Å: Chain D: T.71, A.74, D.75, S.76, M.78 Chain L: R.73, G.102, A.103, S.104, K.126, L.127 Ligand excluded by PLIP CXS.59: 6 residues within 4Å: Chain I: N.31 Chain L: E.27, L.28, A.113, E.117, N.121 Ligand excluded by PLIP

12 x BEF: BERYLLIUM TRIFLUORIDE ION(Covalent)

BEF.5: 8 residues within 4Å: Chain A: D.57, W.58, N.59, V.86, T.87, A.88, K.109 Ligands: MG.1 No protein-ligand interaction detected (PLIP) BEF.10: 8 residues within 4Å: Chain B: D.57, W.58, N.59, V.86, T.87, A.88, K.109 Ligands: MG.6 No protein-ligand interaction detected (PLIP) BEF.15: 8 residues within 4Å: Chain C: D.57, W.58, N.59, V.86, T.87, A.88, K.109 Ligands: MG.11 No protein-ligand interaction detected (PLIP) BEF.20: 8 residues within 4Å: Chain D: D.57, W.58, N.59, V.86, T.87, A.88, K.109 Ligands: MG.16 No protein-ligand interaction detected (PLIP) BEF.25: 8 residues within 4Å: Chain E: D.57, W.58, N.59, V.86, T.87, A.88, K.109 Ligands: MG.21 No protein-ligand interaction detected (PLIP) BEF.30: 8 residues within 4Å: Chain F: D.57, W.58, N.59, V.86, T.87, A.88, K.109 Ligands: MG.26 No protein-ligand interaction detected (PLIP) BEF.35: 8 residues within 4Å: Chain G: D.57, W.58, N.59, V.86, T.87, A.88, K.109 Ligands: MG.31 No protein-ligand interaction detected (PLIP) BEF.40: 8 residues within 4Å: Chain H: D.57, W.58, N.59, V.86, T.87, A.88, K.109 Ligands: MG.36 No protein-ligand interaction detected (PLIP) BEF.45: 8 residues within 4Å: Chain I: D.57, W.58, N.59, V.86, T.87, A.88, K.109 Ligands: MG.41 No protein-ligand interaction detected (PLIP) BEF.50: 8 residues within 4Å: Chain J: D.57, W.58, N.59, V.86, T.87, A.88, K.109 Ligands: MG.46 No protein-ligand interaction detected (PLIP) BEF.55: 8 residues within 4Å: Chain K: D.57, W.58, N.59, V.86, T.87, A.88, K.109 Ligands: MG.51 No protein-ligand interaction detected (PLIP) BEF.60: 8 residues within 4Å: Chain L: D.57, W.58, N.59, V.86, T.87, A.88, K.109 Ligands: MG.56 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guhaniyogi, J. et al., Crystal Structures of Beryllium Fluoride-free and Beryllium Fluoride-bound CheY in Complex with the Conserved C-terminal Peptide of CheZ Reveal Dual Binding Modes Specific to CheY Conformation. J.Mol.Biol. (2006)

Release Date

2006-05-23

Peptides

Chemotaxis protein cheY: 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

Chemotaxis protein cheY

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