SMTL ID : 8trg.1

Structure of full-length LexA bound to a RecA filament

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-8-2-mer

Ligands

8 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.1: 13 residues within 4Å: Chain A: P.94, E.95, S.96, S.97, G.98, K.99, T.100, T.101, D.127, Y.130, S.267, Y.291 Ligands: MG.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:P.94, A:S.96, A:S.97, A:G.98, A:K.99, A:T.100, A:T.101, A:T.101, A:Y.291 Salt bridges: A:K.99 pi-Stacking: A:Y.130 AGS.3: 22 residues within 4Å: Chain A: F.244, K.275, N.276, K.277, I.278, A.279, A.280, P.281, F.282 Chain B: E.95, S.96, S.97, G.98, K.99, T.100, T.101, D.127, Y.130, S.267, I.289, Y.291 Ligands: MG.4 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.96, B:S.97, B:G.98, B:K.99, B:T.100, B:T.101, B:T.101, A:K.275, A:K.277 Salt bridges: B:K.99 pi-Stacking: B:Y.130, B:Y.130 AGS.5: 21 residues within 4Å: Chain B: F.244, K.275, N.276, K.277, I.278, A.279, A.280, P.281 Chain C: E.95, S.96, S.97, G.98, K.99, T.100, T.101, D.127, Y.130, S.267, I.289, Y.291 Ligands: MG.6 12 PLIP interactions: 9 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:S.96, C:K.99, C:T.100, C:T.101, C:T.101, C:Y.291, B:K.275, B:K.277, B:K.277 Salt bridges: C:K.99 pi-Stacking: C:Y.130, C:Y.130 AGS.7: 22 residues within 4Å: Chain C: F.244, K.275, N.276, K.277, I.278, A.279, A.280, P.281 Chain D: E.95, S.96, S.97, G.98, K.99, T.100, T.101, E.123, D.127, Y.130, S.267, I.289, Y.291 Ligands: MG.8 16 PLIP interactions: 11 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:S.96, D:S.97, D:G.98, D:K.99, D:T.100, D:T.101, D:S.267, D:Y.291, C:F.244, C:K.275, C:N.276, C:K.277, C:K.277 Salt bridges: D:K.99 pi-Stacking: D:Y.130, D:Y.130 AGS.9: 22 residues within 4Å: Chain D: F.244, K.275, N.276, K.277, I.278, A.279, A.280, P.281 Chain E: E.95, S.96, S.97, G.98, K.99, T.100, T.101, E.123, D.127, Y.130, S.267, I.289, Y.291 Ligands: MG.10 12 PLIP interactions: 3 interactions with chain D, 9 interactions with chain E Hydrogen bonds: D:K.275, D:N.276, D:K.277, E:S.96, E:S.97, E:G.98, E:K.99, E:T.100, E:T.101, E:E.123 Salt bridges: E:K.99 pi-Stacking: E:Y.130 AGS.11: 21 residues within 4Å: Chain E: F.244, K.275, N.276, K.277, I.278, A.279, A.280, P.281 Chain F: E.95, S.96, S.97, G.98, K.99, T.100, T.101, D.127, Y.130, S.267, I.289, Y.291 Ligands: MG.12 19 PLIP interactions: 12 interactions with chain F, 7 interactions with chain E Hydrogen bonds: F:S.96, F:S.97, F:G.98, F:K.99, F:T.100, F:T.100, F:T.100, F:T.101, F:Y.291, E:F.244, E:K.275, E:N.276, E:K.277, E:K.277 Salt bridges: F:K.99, E:K.277, E:K.277 pi-Stacking: F:Y.130, F:Y.130 AGS.13: 22 residues within 4Å: Chain F: F.244, K.275, N.276, K.277, I.278, A.279, A.280, P.281 Chain G: E.95, S.96, S.97, G.98, K.99, T.100, T.101, D.127, Y.130, K.133, S.267, I.289, Y.291 Ligands: MG.14 15 PLIP interactions: 11 interactions with chain G, 4 interactions with chain F Hydrogen bonds: G:S.96, G:S.97, G:G.98, G:K.99, G:T.100, G:T.101, G:E.123, G:Y.130, F:K.275, F:N.276, F:K.277, F:K.277 Salt bridges: G:K.99 pi-Stacking: G:Y.130, G:Y.130 AGS.15: 21 residues within 4Å: Chain G: F.244, K.275, N.276, K.277, I.278, A.279, A.280, P.281 Chain H: E.95, S.96, S.97, G.98, K.99, T.100, T.101, D.127, Y.130, S.267, I.289, Y.291 Ligands: MG.16 16 PLIP interactions: 11 interactions with chain H, 5 interactions with chain G Hydrogen bonds: H:S.96, H:S.97, H:G.98, H:K.99, H:T.100, H:T.101, H:T.101, H:Y.291, G:F.244, G:K.275, G:N.276, G:K.277, G:I.278 Salt bridges: H:K.99 pi-Stacking: H:Y.130, H:Y.130

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.100 Ligands: AGS.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.100 MG.4: 3 residues within 4Å: Chain A: K.277 Chain B: T.100 Ligands: AGS.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.100 MG.6: 2 residues within 4Å: Chain C: T.100 Ligands: AGS.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.100 MG.8: 3 residues within 4Å: Chain C: K.277 Chain D: T.100 Ligands: AGS.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.100 MG.10: 3 residues within 4Å: Chain E: K.99, T.100 Ligands: AGS.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.100 MG.12: 3 residues within 4Å: Chain E: K.277 Chain F: T.100 Ligands: AGS.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.100 MG.14: 4 residues within 4Å: Chain F: K.277 Chain G: K.99, T.100 Ligands: AGS.13 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.100 MG.16: 3 residues within 4Å: Chain H: K.99, T.100 Ligands: AGS.15 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cory, M.B. et al., The LexA-RecA* structure reveals a lock-and-key mechanism for SOS activation. To Be Published

Release Date

2023-11-15

Peptides

Protein RecA: ABCDEFGH
LexA repressor: IJ

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

Protein RecA

LexA repressor