SMTL ID : 5iun.3 (2 other biounits)

Crystal structure of the DesK-DesR complex in the phosphatase state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

hetero-6-6-mer

Ligands

6 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.1: 17 residues within 4Å: Chain A: E.143, N.147, V.148, K.150, H.151, S.152, D.174, T.177, F.178, K.179, G.180, G.188, H.189, G.190, L.191, T.213 Ligands: MG.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:E.143, A:N.147, A:K.150, A:K.150, A:D.174, A:K.179, A:G.190, A:L.191 pi-Cation interactions: A:H.151 ACP.4: 17 residues within 4Å: Chain B: E.143, N.147, V.148, K.150, H.151, S.152, D.174, T.177, F.178, K.179, G.180, G.188, H.189, G.190, L.191, T.213 Ligands: MG.5 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:E.143, B:N.147, B:K.150, B:D.174, B:K.179, B:H.189, B:G.190, B:L.191, B:T.213 Water bridges: B:E.143, B:N.147 pi-Cation interactions: B:H.151 ACP.11: 18 residues within 4Å: Chain E: E.143, N.147, V.148, K.150, H.151, S.152, D.174, T.177, F.178, K.179, G.180, S.184, G.188, H.189, G.190, L.191, T.213 Ligands: MG.12 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:N.147, E:K.150, E:D.174, E:K.179, E:S.184, E:H.189, E:G.190, E:L.191, E:T.213 pi-Cation interactions: E:H.151 ACP.15: 17 residues within 4Å: Chain G: E.143, N.147, V.148, K.150, H.151, S.152, D.174, T.177, F.178, K.179, G.180, G.188, H.189, G.190, L.191, T.213 Ligands: MG.16 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:E.143, G:E.143, G:N.147, G:K.150, G:K.150, G:D.174, G:K.179, G:H.189, G:G.190, G:L.191, G:T.213 pi-Cation interactions: G:H.151 ACP.18: 17 residues within 4Å: Chain H: E.143, N.147, V.148, K.150, H.151, S.152, D.174, T.177, F.178, K.179, G.180, G.188, H.189, G.190, L.191, T.213 Ligands: MG.19 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:E.143, H:N.147, H:K.150, H:D.174, H:K.179, H:G.190, H:L.191 Water bridges: H:E.143, H:N.147 pi-Cation interactions: H:H.151 ACP.25: 18 residues within 4Å: Chain K: E.143, N.147, V.148, K.150, H.151, S.152, D.174, T.177, F.178, K.179, G.180, S.184, G.188, H.189, G.190, L.191, T.213 Ligands: MG.26 9 PLIP interactions: 9 interactions with chain K Hydrogen bonds: K:E.143, K:N.147, K:K.150, K:D.174, K:K.179, K:S.184, K:G.190, K:L.191 pi-Cation interactions: K:H.151

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.143, N.147 Ligands: ACP.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.143, H2O.1 MG.5: 3 residues within 4Å: Chain B: E.143, N.147 Ligands: ACP.4 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.143, H2O.1 MG.6: 5 residues within 4Å: Chain C: E.12, D.13, D.58, E.60 Ligands: BEF.7 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.13, C:D.58, C:E.60, H2O.1, H2O.1 MG.9: 6 residues within 4Å: Chain D: E.12, D.13, D.58, E.60, K.106 Ligands: BEF.10 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.13, D:D.58, D:E.60, H2O.1, H2O.1 MG.12: 3 residues within 4Å: Chain E: E.143, N.147 Ligands: ACP.11 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.143, H2O.1 MG.13: 5 residues within 4Å: Chain F: E.12, D.13, D.58, E.60 Ligands: BEF.14 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.13, F:D.58, F:E.60, H2O.1, H2O.1 MG.16: 3 residues within 4Å: Chain G: E.143, N.147 Ligands: ACP.15 2 PLIP interactions: 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.143, H2O.1 MG.19: 3 residues within 4Å: Chain H: E.143, N.147 Ligands: ACP.18 2 PLIP interactions: 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.143, H2O.1 MG.20: 5 residues within 4Å: Chain I: E.12, D.13, D.58, E.60 Ligands: BEF.21 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:D.13, I:D.58, I:E.60, H2O.1, H2O.1 MG.23: 6 residues within 4Å: Chain J: E.12, D.13, D.58, E.60, K.106 Ligands: BEF.24 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:D.13, J:D.58, J:E.60, H2O.1, H2O.1 MG.26: 3 residues within 4Å: Chain K: E.143, N.147 Ligands: ACP.25 2 PLIP interactions: 1 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:E.143, H2O.1 MG.27: 5 residues within 4Å: Chain L: E.12, D.13, D.58, E.60 Ligands: BEF.28 5 PLIP interactions: 3 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:D.13, L:D.58, L:E.60, H2O.1, H2O.1

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.3: 6 residues within 4Å: Chain A: Q.69, R.72 Chain F: V.34, G.35, K.36, F.46 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:Q.69, A:R.72, F:K.36 MES.17: 6 residues within 4Å: Chain G: Q.69, R.72 Chain L: V.34, G.35, K.36, F.46 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain L Hydrogen bonds: G:Q.69, G:R.72, L:K.36

6 x BEF: BERYLLIUM TRIFLUORIDE ION(Covalent)

BEF.7: 8 residues within 4Å: Chain A: Q.47 Chain C: D.58, I.59, E.60, T.84, T.85, K.106 Ligands: MG.6 No protein-ligand interaction detected (PLIP) BEF.10: 8 residues within 4Å: Chain B: Q.47 Chain D: D.58, I.59, E.60, T.84, T.85, K.106 Ligands: MG.9 No protein-ligand interaction detected (PLIP) BEF.14: 9 residues within 4Å: Chain E: Q.47 Chain F: D.58, I.59, E.60, L.83, T.84, T.85, K.106 Ligands: MG.13 No protein-ligand interaction detected (PLIP) BEF.21: 8 residues within 4Å: Chain G: Q.47 Chain I: D.58, I.59, E.60, T.84, T.85, K.106 Ligands: MG.20 No protein-ligand interaction detected (PLIP) BEF.24: 8 residues within 4Å: Chain H: Q.47 Chain J: D.58, I.59, E.60, T.84, T.85, K.106 Ligands: MG.23 No protein-ligand interaction detected (PLIP) BEF.28: 9 residues within 4Å: Chain K: Q.47 Chain L: D.58, I.59, E.60, L.83, T.84, T.85, K.106 Ligands: MG.27 No protein-ligand interaction detected (PLIP)

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

SO4.8: 2 residues within 4Å: Chain C: G.99, R.125 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:K.101, C:R.125 SO4.22: 2 residues within 4Å: Chain I: G.99, R.125 2 PLIP interactions: 2 interactions with chain I Salt bridges: I:K.101, I:R.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Trajtenberg, F. et al., Regulation of signaling directionality revealed by 3D snapshots of a kinase:regulator complex in action. Elife (2016)

Release Date

2016-12-21

Peptides

Sensor histidine kinase DesK: ABEGHK
Transcriptional regulatory protein DesR: CDFIJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
E

G
A

H
B

K
E

C
C

D
D

F
F

I
C

J
D

L
F

Sensor histidine kinase DesK

Transcriptional regulatory protein DesR

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