SMTL ID : 6s5b.1

Non-square conformation of KtrA R16K mutant ring with bound ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.05 Å

Oligo State

homo-octamer

Ligands

8 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 18 residues within 4Å: Chain A: G.13, G.15, K.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 Chain B: E.125 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:K.16, A:F.17, A:I.37, A:N.38, A:K.41, A:K.41, A:N.56, A:A.57, A:G.79, A:A.80 Salt bridges: A:K.103 ADP.2: 19 residues within 4Å: Chain A: E.125 Chain B: G.13, L.14, G.15, K.16, F.17, D.36, I.37, N.38, K.41, A.55, N.56, A.57, A.77, I.78, G.79, A.80, K.103, E.125 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:L.14, B:L.14, B:K.16, B:F.17, B:I.37, B:N.38, B:K.41, B:N.56, B:A.57, B:G.79, B:A.80, B:E.125 Salt bridges: B:K.16, B:K.16, B:K.103 ADP.3: 20 residues within 4Å: Chain C: G.13, L.14, G.15, K.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 Chain D: E.125 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:L.14, C:L.14, C:K.16, C:F.17, C:I.37, C:N.38, C:N.56, C:A.57, C:G.79, C:A.80 Salt bridges: C:K.16, C:K.16, C:K.103 ADP.4: 21 residues within 4Å: Chain C: E.125 Chain D: I.12, G.13, L.14, G.15, K.16, F.17, G.18, D.36, I.37, N.38, K.41, A.55, N.56, A.57, T.58, A.77, I.78, G.79, A.80, K.103 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:L.14, D:K.16, D:F.17, D:G.18, D:I.37, D:N.38, D:K.41, D:N.56, D:A.57, D:G.79, D:A.80 Salt bridges: D:K.16, D:K.16, D:K.103 ADP.5: 19 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, A.77, I.78, G.79, K.103 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:L.14, E:G.15, E:K.16, E:F.17, E:G.18, E:I.37, E:K.41, E:K.41, E:N.56, E:A.57, E:G.79 Salt bridges: E:K.16, E:K.16, E:K.103 ADP.6: 18 residues within 4Å: Chain E: E.125 Chain F: G.13, L.14, G.15, K.16, F.17, D.36, I.37, N.38, K.41, A.55, N.56, A.57, A.77, I.78, G.79, A.80, K.103 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:K.16, F:F.17, F:I.37, F:N.56, F:A.57, F:G.79, F:A.80 Salt bridges: F:K.16, F:K.16, F:K.103 ADP.7: 16 residues within 4Å: Chain G: G.13, G.15, K.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, K.103 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:K.16, G:F.17, G:I.37, G:N.38, G:N.56, G:A.57, G:T.58, G:G.79, G:A.80 Salt bridges: G:K.16, G:K.16, G:K.103 ADP.8: 19 residues within 4Å: Chain G: E.125 Chain H: G.13, L.14, G.15, K.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, K.103 15 PLIP interactions: 15 interactions with chain H Hydrogen bonds: H:L.14, H:L.14, H:K.16, H:F.17, H:I.37, H:N.38, H:K.41, H:N.56, H:A.57, H:G.79, H:A.80, H:E.125 Salt bridges: H:K.16, H:K.16, H:K.103

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
G

D
H

E
C

F
D

G
E

H
F

Ktr system potassium uptake protein A

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