SMTL ID : 8k1k.1

KtrA bound with ATP and sodium

Coordinates

PDB Format Compare

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, N.81, K.103, E.125 Chain B: R.16, E.125 Ligands: NA.3 19 PLIP interactions: 16 interactions with chain A, 3 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:T.58, A:G.79, A:A.80, A:N.81, A:E.125, B:E.125 Salt bridges: A:R.16, A:K.103, A:K.103, B:R.16, B:R.16 ATP.2: 23 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, N.81, A.84, K.103, E.125 Ligands: NA.3 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain A Hydrogen bonds: 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:G.79, B:A.80, B:N.81, A:R.16 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, N.81, K.103, E.125 Chain D: R.16, E.125 Ligands: NA.6 19 PLIP interactions: 3 interactions with chain D, 16 interactions with chain C Hydrogen bonds: D:E.125, 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:T.58, C:G.79, C:A.80, C:N.81, C:E.125 Salt bridges: D:R.16, D:R.16, C:R.16, C:K.103, C:K.103 ATP.5: 23 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, N.81, A.84, K.103, E.125 Ligands: NA.6 16 PLIP interactions: 14 interactions with chain D, 2 interactions with chain C Hydrogen bonds: 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:G.79, D:A.80, D:N.81, C:R.16 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, N.81, K.103, E.125 Chain F: R.16, E.125 Ligands: NA.9 19 PLIP interactions: 3 interactions with chain F, 16 interactions with chain E Hydrogen bonds: F:E.125, 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:T.58, E:G.79, E:A.80, E:N.81, E:E.125 Salt bridges: F:R.16, F:R.16, E:R.16, E:K.103, E:K.103 ATP.8: 23 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, N.81, A.84, K.103, E.125 Ligands: NA.9 16 PLIP interactions: 14 interactions with chain F, 2 interactions with chain E Hydrogen bonds: 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:G.79, F:A.80, F:N.81, E:R.16 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, N.81, K.103, E.125 Chain H: R.16, E.125 Ligands: NA.12 19 PLIP interactions: 16 interactions with chain G, 3 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:T.58, G:G.79, G:A.80, G:N.81, G:E.125, H:E.125 Salt bridges: G:R.16, G:K.103, G:K.103, H:R.16, H:R.16 ATP.11: 23 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, N.81, A.84, K.103, E.125 Ligands: NA.12 16 PLIP interactions: 14 interactions with chain H, 2 interactions with chain G Hydrogen bonds: 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:G.79, H:A.80, H:N.81, G:R.16 Salt bridges: H:R.16, H:K.103, H:K.103, G:R.16

4 x NA: SODIUM ION(Non-functional Binders)

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chiang, W.T. et al., Structural basis and synergism of ATP and Na + activation in bacterial K + uptake system KtrAB. Nat Commun (2024)

Release Date

2024-04-03

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

Related Entries With Identical Sequence