SMTL ID : 6s5c.1

Square conformation of KtrA WT ring with bound ATP and calcium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-octamer

Ligands

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

ATP.1: 23 residues within 4Å: Chain A: G.13, L.14, G.15, R.16, F.17, D.36, I.37, N.38, K.41, A.55, N.56, A.57, T.58, A.77, I.78, G.79, A.80, A.84, K.103, E.125 Chain B: R.16, E.125 Ligands: CA.2 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:L.14, A:R.16, A:F.17, A:I.37, A:N.38, A:K.41, A:N.56, A:A.57, A:G.79, A:A.80, A:N.81, B:R.16 Salt bridges: A:R.16, A:K.103, A:K.103, B:R.16 ATP.3: 22 residues within 4Å: Chain A: R.16, E.125 Chain B: G.13, L.14, G.15, R.16, F.17, D.36, I.37, N.38, K.41, A.55, N.56, A.57, T.58, I.78, G.79, A.80, A.84, K.103, E.125 Ligands: CA.2 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.14, B:L.14, B:R.16, B:F.17, B:I.37, B:N.38, B:K.41, B:A.57, B:T.58, B:T.58, B:G.79, B:A.80 Salt bridges: B:R.16, B:K.103, B:K.103, A:R.16 ATP.4: 23 residues within 4Å: Chain C: G.13, L.14, G.15, R.16, F.17, D.36, I.37, N.38, K.41, A.55, N.56, A.57, T.58, A.77, I.78, G.79, A.80, A.84, K.103, E.125 Chain D: R.16, E.125 Ligands: CA.5 16 PLIP interactions: 14 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:L.14, C:R.16, C:F.17, C:I.37, C:N.38, C:K.41, C:N.56, C:A.57, C:G.79, C:A.80, C:N.81, D:R.16 Salt bridges: C:R.16, C:K.103, C:K.103, D:R.16 ATP.6: 22 residues within 4Å: Chain C: R.16, E.125 Chain D: G.13, L.14, G.15, R.16, F.17, D.36, I.37, N.38, K.41, A.55, N.56, A.57, T.58, I.78, G.79, A.80, A.84, K.103, E.125 Ligands: CA.5 16 PLIP interactions: 15 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:L.14, D:L.14, D:R.16, D:F.17, D:I.37, D:N.38, D:K.41, D:A.57, D:T.58, D:T.58, D:G.79, D:A.80 Salt bridges: D:R.16, D:K.103, D:K.103, C:R.16 ATP.7: 23 residues within 4Å: Chain E: G.13, L.14, G.15, R.16, F.17, D.36, I.37, N.38, K.41, A.55, N.56, A.57, T.58, A.77, I.78, G.79, A.80, A.84, K.103, E.125 Chain F: R.16, E.125 Ligands: CA.8 16 PLIP interactions: 14 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:L.14, E:R.16, E:F.17, E:I.37, E:N.38, E:K.41, E:N.56, E:A.57, E:G.79, E:A.80, E:N.81, F:R.16 Salt bridges: E:R.16, E:K.103, E:K.103, F:R.16 ATP.9: 22 residues within 4Å: Chain E: R.16, E.125 Chain F: G.13, L.14, G.15, R.16, F.17, D.36, I.37, N.38, K.41, A.55, N.56, A.57, T.58, I.78, G.79, A.80, A.84, K.103, E.125 Ligands: CA.8 16 PLIP interactions: 15 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:L.14, F:L.14, F:R.16, F:F.17, F:I.37, F:N.38, F:K.41, F:A.57, F:T.58, F:T.58, F:G.79, F:A.80 Salt bridges: F:R.16, F:K.103, F:K.103, E:R.16 ATP.10: 23 residues within 4Å: Chain G: G.13, L.14, G.15, R.16, F.17, D.36, I.37, N.38, K.41, A.55, N.56, A.57, T.58, A.77, I.78, G.79, A.80, A.84, K.103, E.125 Chain H: R.16, E.125 Ligands: CA.11 16 PLIP interactions: 14 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:L.14, G:R.16, G:F.17, G:I.37, G:N.38, G:K.41, G:N.56, G:A.57, G:G.79, G:A.80, G:N.81, H:R.16 Salt bridges: G:R.16, G:K.103, G:K.103, H:R.16 ATP.12: 22 residues within 4Å: Chain G: R.16, E.125 Chain H: G.13, L.14, G.15, R.16, F.17, D.36, I.37, N.38, K.41, A.55, N.56, A.57, T.58, I.78, G.79, A.80, A.84, K.103, E.125 Ligands: CA.11 16 PLIP interactions: 15 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:L.14, H:L.14, H:R.16, H:F.17, H:I.37, H:N.38, H:K.41, H:A.57, H:T.58, H:T.58, H:G.79, H:A.80 Salt bridges: H:R.16, H:K.103, H:K.103, G:R.16

4 x CA: CALCIUM ION(Non-covalent)

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

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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