SMTL ID : 6q7m.1

Spiral structure of E. coli RavA in the RavA-LdcI cage-like complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-20-6-mer

Ligands

20 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 13 residues within 4Å: Chain A: G.219, T.220, S.221, H.245, S.247, D.330, A.332, W.333, H.366, K.367 Chain F: T.398, T.399, S.400 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain F Hydrophobic interactions: A:H.245, A:A.332, A:K.367 Hydrogen bonds: A:T.220, A:S.221, A:S.221, A:S.247, A:W.333, F:T.398, F:T.399, F:S.400 Salt bridges: A:H.366, A:K.367 pi-Stacking: A:H.245 PLP.2: 12 residues within 4Å: Chain B: G.219, T.220, S.221, H.245, D.330, A.332, W.333, H.366, K.367 Chain I: T.398, T.399, S.400 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain I Hydrophobic interactions: B:A.332, B:K.367 Hydrogen bonds: B:T.220, B:S.221, B:W.333, I:S.400, I:S.400 Salt bridges: B:H.366, B:K.367 pi-Stacking: B:H.245 PLP.3: 12 residues within 4Å: Chain C: G.219, T.220, S.221, H.245, D.330, A.332, W.333, H.366, K.367 Chain G: T.398, T.399, S.400 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain G Hydrophobic interactions: C:A.332, C:K.367 Hydrogen bonds: C:T.220, C:S.221, C:W.333, G:S.400, G:S.400 Salt bridges: C:H.366, C:K.367 pi-Stacking: C:H.245 PLP.4: 12 residues within 4Å: Chain D: G.219, T.220, S.221, H.245, D.330, A.332, W.333, H.366, K.367 Chain J: T.398, T.399, S.400 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain J Hydrophobic interactions: D:A.332, D:K.367 Hydrogen bonds: D:T.220, D:S.221, D:W.333, J:S.400 Salt bridges: D:H.366, D:K.367 pi-Stacking: D:H.245 PLP.5: 12 residues within 4Å: Chain E: G.219, T.220, S.221, H.245, D.330, A.332, W.333, H.366, K.367 Chain H: T.398, T.399, S.400 12 PLIP interactions: 9 interactions with chain E, 3 interactions with chain H Hydrophobic interactions: E:H.245, E:A.332, E:K.367 Hydrogen bonds: E:T.220, E:S.221, E:W.333, H:T.398, H:S.400, H:S.400 Salt bridges: E:H.366, E:K.367 pi-Stacking: E:H.245 PLP.6: 12 residues within 4Å: Chain A: T.398, T.399, S.400 Chain F: G.219, T.220, S.221, H.245, D.330, A.332, W.333, H.366, K.367 14 PLIP interactions: 12 interactions with chain F, 2 interactions with chain A Hydrophobic interactions: F:H.245, F:A.332, F:K.367 Hydrogen bonds: F:T.220, F:T.220, F:T.220, F:S.221, F:W.333, F:K.367, A:T.399, A:T.399 Salt bridges: F:H.366, F:K.367 pi-Stacking: F:H.245 PLP.7: 12 residues within 4Å: Chain C: T.398, T.399, S.400 Chain G: G.219, T.220, S.221, H.245, D.330, A.332, W.333, H.366, K.367 15 PLIP interactions: 4 interactions with chain C, 11 interactions with chain G Hydrogen bonds: C:T.398, C:T.399, C:T.399, C:S.400, G:T.220, G:T.220, G:T.220, G:S.221, G:W.333, G:K.367 Hydrophobic interactions: G:A.332, G:K.367 Salt bridges: G:H.366, G:K.367 pi-Stacking: G:H.245 PLP.8: 12 residues within 4Å: Chain E: T.398, T.399, S.400 Chain H: G.219, T.220, S.221, H.245, D.330, A.332, W.333, H.366, K.367 15 PLIP interactions: 11 interactions with chain H, 4 interactions with chain E Hydrophobic interactions: H:A.332, H:K.367 Hydrogen bonds: H:T.220, H:T.220, H:T.220, H:S.221, H:W.333, H:K.367, E:T.398, E:T.399, E:T.399, E:S.400 Salt bridges: H:H.366, H:K.367 pi-Stacking: H:H.245 PLP.9: 12 residues within 4Å: Chain B: T.398, T.399, S.400 Chain I: G.219, T.220, S.221, H.245, D.330, A.332, W.333, H.366, K.367 12 PLIP interactions: 2 interactions with chain B, 10 interactions with chain I Hydrogen bonds: B:T.398, B:S.400, I:T.220, I:T.220, I:T.220, I:S.221, I:K.367 Hydrophobic interactions: I:A.332, I:K.367 Salt bridges: I:H.366, I:K.367 pi-Stacking: I:H.245 PLP.10: 12 residues within 4Å: Chain D: T.398, T.399, S.400 Chain J: G.219, T.220, S.221, H.245, D.330, A.332, W.333, H.366, K.367 15 PLIP interactions: 4 interactions with chain D, 11 interactions with chain J Hydrogen bonds: D:T.398, D:T.399, D:T.399, D:S.400, J:T.220, J:T.220, J:T.220, J:S.221, J:W.333, J:K.367 Hydrophobic interactions: J:A.332, J:K.367 Salt bridges: J:H.366, J:K.367 pi-Stacking: J:H.245 PLP.11: 13 residues within 4Å: Chain K: G.219, T.220, S.221, H.245, S.247, D.330, A.332, W.333, H.366, K.367 Chain R: T.398, T.399, S.400 16 PLIP interactions: 12 interactions with chain K, 4 interactions with chain R Hydrophobic interactions: K:H.245, K:A.332, K:K.367 Hydrogen bonds: K:T.220, K:T.220, K:T.220, K:S.221, K:W.333, K:K.367, R:T.398, R:T.399, R:T.399, R:S.400 Salt bridges: K:H.366, K:K.367 pi-Stacking: K:H.245 PLP.12: 12 residues within 4Å: Chain L: G.219, T.220, S.221, H.245, D.330, A.332, W.333, H.366, K.367 Chain Q: T.398, T.399, S.400 15 PLIP interactions: 11 interactions with chain L, 4 interactions with chain Q Hydrophobic interactions: L:A.332, L:K.367 Hydrogen bonds: L:T.220, L:T.220, L:T.220, L:S.221, L:W.333, L:K.367, Q:T.398, Q:T.399, Q:T.399, Q:S.400 Salt bridges: L:H.366, L:K.367 pi-Stacking: L:H.245 PLP.13: 12 residues within 4Å: Chain M: G.219, T.220, S.221, H.245, D.330, A.332, W.333, H.366, K.367 Chain P: T.398, T.399, S.400 14 PLIP interactions: 11 interactions with chain M, 3 interactions with chain P Hydrophobic interactions: M:A.332, M:K.367 Hydrogen bonds: M:T.220, M:T.220, M:T.220, M:S.221, M:W.333, M:K.367, P:T.399, P:T.399, P:S.400 Salt bridges: M:H.366, M:K.367 pi-Stacking: M:H.245 PLP.14: 12 residues within 4Å: Chain N: G.219, T.220, S.221, H.245, D.330, A.332, W.333, H.366, K.367 Chain T: T.398, T.399, S.400 12 PLIP interactions: 10 interactions with chain N, 2 interactions with chain T Hydrophobic interactions: N:A.332, N:K.367 Hydrogen bonds: N:T.220, N:T.220, N:T.220, N:S.221, N:K.367, T:T.398, T:S.400 Salt bridges: N:H.366, N:K.367 pi-Stacking: N:H.245 PLP.15: 12 residues within 4Å: Chain O: G.219, T.220, S.221, H.245, D.330, A.332, W.333, H.366, K.367 Chain S: T.398, T.399, S.400 15 PLIP interactions: 11 interactions with chain O, 4 interactions with chain S Hydrophobic interactions: O:A.332, O:K.367 Hydrogen bonds: O:T.220, O:T.220, O:T.220, O:S.221, O:W.333, O:K.367, S:T.398, S:T.399, S:T.399, S:S.400 Salt bridges: O:H.366, O:K.367 pi-Stacking: O:H.245 PLP.16: 12 residues within 4Å: Chain M: T.398, T.399, S.400 Chain P: G.219, T.220, S.221, H.245, D.330, A.332, W.333, H.366, K.367 12 PLIP interactions: 3 interactions with chain M, 9 interactions with chain P Hydrogen bonds: M:T.398, M:S.400, M:S.400, P:T.220, P:S.221, P:W.333 Hydrophobic interactions: P:H.245, P:A.332, P:K.367 Salt bridges: P:H.366, P:K.367 pi-Stacking: P:H.245 PLP.17: 12 residues within 4Å: Chain L: T.398, T.399, S.400 Chain Q: G.219, T.220, S.221, H.245, D.330, A.332, W.333, H.366, K.367 10 PLIP interactions: 8 interactions with chain Q, 2 interactions with chain L Hydrophobic interactions: Q:A.332, Q:K.367 Hydrogen bonds: Q:T.220, Q:S.221, Q:W.333, L:S.400, L:S.400 Salt bridges: Q:H.366, Q:K.367 pi-Stacking: Q:H.245 PLP.18: 12 residues within 4Å: Chain K: T.398, T.399, S.400 Chain R: G.219, T.220, S.221, H.245, D.330, A.332, W.333, H.366, K.367 11 PLIP interactions: 9 interactions with chain R, 2 interactions with chain K Hydrophobic interactions: R:H.245, R:A.332, R:K.367 Hydrogen bonds: R:T.220, R:S.221, R:W.333, K:T.398, K:S.400 Salt bridges: R:H.366, R:K.367 pi-Stacking: R:H.245 PLP.19: 12 residues within 4Å: Chain O: T.398, T.399, S.400 Chain S: G.219, T.220, S.221, H.245, D.330, A.332, W.333, H.366, K.367 9 PLIP interactions: 8 interactions with chain S, 1 interactions with chain O Hydrophobic interactions: S:A.332, S:K.367 Hydrogen bonds: S:T.220, S:S.221, S:W.333, O:S.400 Salt bridges: S:H.366, S:K.367 pi-Stacking: S:H.245 PLP.20: 12 residues within 4Å: Chain N: T.398, T.399, S.400 Chain T: G.219, T.220, S.221, H.245, D.330, A.332, W.333, H.366, K.367 10 PLIP interactions: 8 interactions with chain T, 2 interactions with chain N Hydrophobic interactions: T:A.332, T:K.367 Hydrogen bonds: T:T.220, T:S.221, T:W.333, N:S.400, N:S.400 Salt bridges: T:H.366, T:K.367 pi-Stacking: T:H.245

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

ADP.21: 18 residues within 4Å: Chain U: R.170, D.250, R.251, K.254 Chain V: G.21, L.22, Y.23, R.25, P.48, G.49, I.50, A.51, K.52, S.53, L.54, V.180, M.189, E.196 13 PLIP interactions: 8 interactions with chain V, 5 interactions with chain U Hydrogen bonds: V:Y.23, V:G.49, V:I.50, V:A.51, V:K.52, V:S.53, V:E.196, U:D.250, U:R.251, U:K.254 Salt bridges: V:K.52, U:R.170, U:R.251 ADP.22: 16 residues within 4Å: Chain V: R.170, D.250, R.251, K.254 Chain W: G.21, L.22, R.25, P.48, G.49, I.50, A.51, K.52, S.53, L.54, M.189, E.196 13 PLIP interactions: 5 interactions with chain V, 8 interactions with chain W Hydrogen bonds: V:D.250, V:K.254, W:Y.23, W:G.49, W:I.50, W:A.51, W:K.52, W:S.53, W:L.54 Salt bridges: V:R.170, V:R.251, V:R.251, W:K.52 ADP.23: 17 residues within 4Å: Chain W: R.170, D.250, R.251, K.254 Chain X: G.21, L.22, R.25, P.48, G.49, I.50, A.51, K.52, S.53, L.54, V.180, M.189, E.196 12 PLIP interactions: 5 interactions with chain W, 7 interactions with chain X Hydrogen bonds: W:D.250, W:K.254, X:G.49, X:I.50, X:A.51, X:K.52, X:S.53, X:L.54 Salt bridges: W:R.170, W:R.251, W:R.251, X:K.52 ADP.24: 17 residues within 4Å: Chain X: R.170, D.250, R.251, K.254 Chain Y: L.22, Y.23, R.25, P.48, G.49, I.50, A.51, K.52, S.53, L.54, V.180, M.189, E.196 14 PLIP interactions: 8 interactions with chain Y, 6 interactions with chain X Hydrogen bonds: Y:G.49, Y:I.50, Y:A.51, Y:K.52, Y:S.53, Y:S.53, Y:L.54, X:D.250, X:D.250, X:K.254 Salt bridges: Y:K.52, X:R.170, X:R.251, X:R.251 ADP.25: 17 residues within 4Å: Chain Y: R.170, D.250, R.251, K.254 Chain Z: L.22, Y.23, R.25, P.48, G.49, I.50, A.51, K.52, S.53, L.54, V.180, M.189, E.196 15 PLIP interactions: 9 interactions with chain Z, 6 interactions with chain Y Hydrogen bonds: Z:Y.23, Z:G.49, Z:I.50, Z:A.51, Z:K.52, Z:S.53, Z:S.53, Z:L.54, Y:D.250, Y:D.250, Y:R.251, Y:K.254 Salt bridges: Z:K.52, Y:R.170, Y:R.251

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jessop, M. et al., Structural insights into ATP hydrolysis by the MoxR ATPase RavA and the LdcI-RavA cage-like complex. Commun Biol (2020)

Release Date

2020-02-12

Peptides

Inducible lysine decarboxylase: ABCDEFGHIJKLMNOPQRST
ATPase RavA: UVWXYZ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

U
U

V
V

W
W

X
X

Y
Y

Z
Z

Inducible lysine decarboxylase

ATPase RavA

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