SMTL ID : 6s2j.1

Square conformation of KtrA R16K mutant ring with bound ATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.67 Å

Oligo State

homo-octamer

Ligands

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

ATP.1: 28 residues within 4Å: Chain A: I.12, G.13, L.14, G.15, K.16, F.17, G.18, V.35, D.36, I.37, N.38, K.41, A.55, N.56, A.57, T.58, A.77, I.78, G.79, A.80, N.81, A.84, K.103, Q.105, E.125 Chain B: K.16, E.125 Ligands: MG.3 21 PLIP interactions: 18 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:K.16, A:F.17, A:D.36, A:D.36, A:I.37, A:N.38, A:K.41, A:N.56, A:A.57, A:G.79, A:A.80, A:Q.105, B:E.125, B:E.125 Water bridges: A:K.16, A:K.16, B:K.16 Salt bridges: A:K.16, A:K.16, A:K.103, A:K.103 ATP.2: 28 residues within 4Å: Chain A: K.16, E.125 Chain B: I.12, G.13, L.14, G.15, K.16, F.17, G.18, V.35, D.36, I.37, N.38, K.41, A.55, N.56, A.57, T.58, A.77, I.78, G.79, A.80, N.81, A.84, K.103, Q.105, E.125 Ligands: MG.3 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.16, B:F.17, B:D.36, B:D.36, B:I.37, B:K.41, B:N.56, B:A.57, B:G.79, B:A.80, B:Q.105, B:E.125, A:E.125 Water bridges: B:K.16, B:K.16, A:K.16 Salt bridges: B:K.16, B:K.16, B:K.103, B:K.103 ATP.4: 28 residues within 4Å: Chain C: I.12, G.13, L.14, G.15, K.16, F.17, G.18, V.35, D.36, I.37, N.38, K.41, A.55, N.56, A.57, T.58, A.77, I.78, G.79, A.80, N.81, A.84, K.103, Q.105, E.125 Chain D: K.16, E.125 Ligands: MG.6 21 PLIP interactions: 18 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:K.16, C:F.17, C:D.36, C:D.36, C:I.37, C:N.38, C:K.41, C:N.56, C:A.57, C:G.79, C:A.80, C:Q.105, D:E.125, D:E.125 Water bridges: C:K.16, C:K.16, D:K.16 Salt bridges: C:K.16, C:K.16, C:K.103, C:K.103 ATP.5: 28 residues within 4Å: Chain C: K.16, E.125 Chain D: I.12, G.13, L.14, G.15, K.16, F.17, G.18, V.35, D.36, I.37, N.38, K.41, A.55, N.56, A.57, T.58, A.77, I.78, G.79, A.80, N.81, A.84, K.103, Q.105, E.125 Ligands: MG.6 20 PLIP interactions: 18 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:K.16, D:F.17, D:D.36, D:D.36, D:I.37, D:K.41, D:N.56, D:A.57, D:G.79, D:A.80, D:Q.105, D:E.125, C:E.125 Water bridges: D:K.16, D:K.16, C:K.16 Salt bridges: D:K.16, D:K.16, D:K.103, D:K.103 ATP.7: 28 residues within 4Å: Chain E: I.12, G.13, L.14, G.15, K.16, F.17, G.18, V.35, D.36, I.37, N.38, K.41, A.55, N.56, A.57, T.58, A.77, I.78, G.79, A.80, N.81, A.84, K.103, Q.105, E.125 Chain F: K.16, E.125 Ligands: MG.9 21 PLIP interactions: 3 interactions with chain F, 18 interactions with chain E Hydrogen bonds: F:E.125, F:E.125, E:K.16, E:F.17, E:D.36, E:D.36, E:I.37, E:N.38, E:K.41, E:N.56, E:A.57, E:G.79, E:A.80, E:Q.105 Water bridges: F:K.16, E:K.16, E:K.16 Salt bridges: E:K.16, E:K.16, E:K.103, E:K.103 ATP.8: 28 residues within 4Å: Chain E: K.16, E.125 Chain F: I.12, G.13, L.14, G.15, K.16, F.17, G.18, V.35, D.36, I.37, N.38, K.41, A.55, N.56, A.57, T.58, A.77, I.78, G.79, A.80, N.81, A.84, K.103, Q.105, E.125 Ligands: MG.9 20 PLIP interactions: 18 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:K.16, F:F.17, F:D.36, F:D.36, F:I.37, F:K.41, F:N.56, F:A.57, F:G.79, F:A.80, F:Q.105, F:E.125, E:E.125 Water bridges: F:K.16, F:K.16, E:K.16 Salt bridges: F:K.16, F:K.16, F:K.103, F:K.103 ATP.10: 28 residues within 4Å: Chain G: I.12, G.13, L.14, G.15, K.16, F.17, G.18, V.35, D.36, I.37, N.38, K.41, A.55, N.56, A.57, T.58, A.77, I.78, G.79, A.80, N.81, A.84, K.103, Q.105, E.125 Chain H: K.16, E.125 Ligands: MG.12 21 PLIP interactions: 18 interactions with chain G, 3 interactions with chain H Hydrogen bonds: G:K.16, G:F.17, G:D.36, G:D.36, G:I.37, G:N.38, G:K.41, G:N.56, G:A.57, G:G.79, G:A.80, G:Q.105, H:E.125, H:E.125 Water bridges: G:K.16, G:K.16, H:K.16 Salt bridges: G:K.16, G:K.16, G:K.103, G:K.103 ATP.11: 28 residues within 4Å: Chain G: K.16, E.125 Chain H: I.12, G.13, L.14, G.15, K.16, F.17, G.18, V.35, D.36, I.37, N.38, K.41, A.55, N.56, A.57, T.58, A.77, I.78, G.79, A.80, N.81, A.84, K.103, Q.105, E.125 Ligands: MG.12 20 PLIP interactions: 18 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:K.16, H:F.17, H:D.36, H:D.36, H:I.37, H:K.41, H:N.56, H:A.57, H:G.79, H:A.80, H:Q.105, H:E.125, G:E.125 Water bridges: H:K.16, H:K.16, G:K.16 Salt bridges: H:K.16, H:K.16, H:K.103, H:K.103

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 8 residues within 4Å: Chain A: K.16, K.103, E.125 Chain B: K.16, K.103, E.125 Ligands: ATP.1, ATP.2 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:E.125, A:E.125, H2O.1, H2O.1 MG.6: 8 residues within 4Å: Chain C: K.16, K.103, E.125 Chain D: K.16, K.103, E.125 Ligands: ATP.4, ATP.5 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:E.125, D:E.125, H2O.1, H2O.1 MG.9: 8 residues within 4Å: Chain E: K.16, K.103, E.125 Chain F: K.16, K.103, E.125 Ligands: ATP.7, ATP.8 4 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: F:E.125, E:E.125, H2O.1, H2O.1 MG.12: 8 residues within 4Å: Chain G: K.16, K.103, E.125 Chain H: K.16, K.103, E.125 Ligands: ATP.10, ATP.11 4 PLIP interactions: 1 interactions with chain G, 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: G:E.125, H:E.125, H2O.1, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Teixeira-Duarte, C.M. et al., Activation of a nucleotide-dependent RCK domain requires binding of a cation cofactor to a conserved site. Elife (2019)

Release Date

2020-01-08

Peptides

Ktr system potassium uptake protein A: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

Ktr system potassium uptake protein A

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