SMTL ID : 7tf6.1

S. aureus GS(12)-Q-GlnR peptide

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-12-12-mer

Ligands

24 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: E.139, E.194, E.201 Ligands: GLN.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.139, A:E.201 MG.2: 3 residues within 4Å: Chain A: E.137, H.250, E.338 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.137, A:H.250, A:E.338 MG.4: 4 residues within 4Å: Chain B: E.139, E.194, E.201 Ligands: GLN.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.139, B:E.201 MG.5: 3 residues within 4Å: Chain B: E.137, H.250, E.338 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.137, B:E.338 MG.7: 4 residues within 4Å: Chain C: E.139, E.194, E.201 Ligands: GLN.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.139, C:E.201 MG.8: 3 residues within 4Å: Chain C: E.137, H.250, E.338 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.137, C:H.250, C:E.338 MG.10: 4 residues within 4Å: Chain F: E.139, E.194, E.201 Ligands: GLN.12 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:E.139, F:E.201 MG.11: 3 residues within 4Å: Chain F: E.137, H.250, E.338 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.137, F:H.250, F:E.338 MG.13: 4 residues within 4Å: Chain G: E.139, E.194, E.201 Ligands: GLN.15 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:E.139, G:E.201 MG.14: 3 residues within 4Å: Chain G: E.137, H.250, E.338 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.137, G:H.250, G:E.338 MG.16: 4 residues within 4Å: Chain H: E.139, E.194, E.201 Ligands: GLN.18 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:E.139, H:E.201 MG.17: 3 residues within 4Å: Chain H: E.137, H.250, E.338 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.137, H:H.250, H:E.338 MG.19: 4 residues within 4Å: Chain L: E.139, E.194, E.201 Ligands: GLN.21 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:E.139, L:E.201 MG.20: 3 residues within 4Å: Chain L: E.137, H.250, E.338 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:E.137, L:H.250, L:E.338 MG.22: 4 residues within 4Å: Chain N: E.139, E.194, E.201 Ligands: GLN.24 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:E.139, N:E.201 MG.23: 3 residues within 4Å: Chain N: E.137, H.250, E.338 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:E.137, N:H.250, N:E.338 MG.25: 4 residues within 4Å: Chain O: E.139, E.194, E.201 Ligands: GLN.27 2 PLIP interactions: 2 interactions with chain O Metal complexes: O:E.139, O:E.201 MG.26: 3 residues within 4Å: Chain O: E.137, H.250, E.338 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:E.137, O:H.250, O:E.338 MG.28: 4 residues within 4Å: Chain R: E.139, E.194, E.201 Ligands: GLN.30 2 PLIP interactions: 2 interactions with chain R Metal complexes: R:E.139, R:E.201 MG.29: 3 residues within 4Å: Chain R: E.137, H.250, E.338 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:E.137, R:H.250, R:E.338 MG.31: 4 residues within 4Å: Chain S: E.139, E.194, E.201 Ligands: GLN.33 2 PLIP interactions: 2 interactions with chain S Metal complexes: S:E.139, S:E.201 MG.32: 3 residues within 4Å: Chain S: E.137, H.250, E.338 3 PLIP interactions: 3 interactions with chain S Metal complexes: S:E.137, S:H.250, S:E.338 MG.34: 4 residues within 4Å: Chain T: E.139, E.194, E.201 Ligands: GLN.36 2 PLIP interactions: 2 interactions with chain T Metal complexes: T:E.139, T:E.201 MG.35: 3 residues within 4Å: Chain T: E.137, H.250, E.338 3 PLIP interactions: 3 interactions with chain T Metal complexes: T:E.137, T:H.250, T:E.338

12 x GLN: GLUTAMINE(Non-covalent)

GLN.3: 17 residues within 4Å: Chain A: E.139, Y.161, E.194, V.195, Q.199, N.245, G.246, S.247, G.248, H.250, R.303, Y.308, E.309, R.340 Chain H: D.58, R.67 Ligands: MG.1 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:E.139, A:Q.199, A:N.245, A:E.309, Q.3 Salt bridges: A:H.250, A:R.303 GLN.6: 17 residues within 4Å: Chain A: D.58, R.67 Chain B: E.139, Y.161, E.194, V.195, Q.199, N.245, G.246, S.247, G.248, H.250, R.303, Y.308, E.309, R.340 Ligands: MG.4 8 PLIP interactions: 1 Ligand-Ligand interactions, 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: Q.6, B:E.139, B:Q.199, B:N.245, B:E.309, A:R.67 Salt bridges: B:H.250, B:R.303 GLN.9: 17 residues within 4Å: Chain B: D.58, R.67 Chain C: E.139, Y.161, E.194, V.195, Q.199, N.245, G.246, S.247, G.248, H.250, R.303, Y.308, E.309, R.340 Ligands: MG.7 8 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: C:E.139, C:Q.199, C:N.245, C:E.309, B:R.67, Q.9 Salt bridges: C:H.250, C:R.303 GLN.12: 17 residues within 4Å: Chain C: D.58, R.67 Chain F: E.139, Y.161, E.194, V.195, Q.199, N.245, G.246, S.247, G.248, H.250, R.303, Y.308, E.309, R.340 Ligands: MG.10 7 PLIP interactions: 6 interactions with chain F, 1 Ligand-Ligand interactions Hydrogen bonds: F:E.139, F:Q.199, F:N.245, F:E.309, Q.12 Salt bridges: F:H.250, F:R.303 GLN.15: 17 residues within 4Å: Chain F: D.58, R.67 Chain G: E.139, Y.161, E.194, V.195, Q.199, N.245, G.246, S.247, G.248, H.250, R.303, Y.308, E.309, R.340 Ligands: MG.13 8 PLIP interactions: 6 interactions with chain G, 1 interactions with chain F, 1 Ligand-Ligand interactions Hydrogen bonds: G:E.139, G:Q.199, G:N.245, G:E.309, F:R.67, Q.15 Salt bridges: G:H.250, G:R.303 GLN.18: 16 residues within 4Å: Chain G: R.67 Chain H: E.139, Y.161, E.194, V.195, Q.199, N.245, G.246, S.247, G.248, H.250, R.303, Y.308, E.309, R.340 Ligands: MG.16 8 PLIP interactions: 6 interactions with chain H, 1 Ligand-Ligand interactions, 1 interactions with chain G Hydrogen bonds: H:E.139, H:Q.199, H:N.245, H:E.309, Q.18, G:R.67 Salt bridges: H:H.250, H:R.303 GLN.21: 17 residues within 4Å: Chain L: E.139, Y.161, E.194, V.195, Q.199, N.245, G.246, S.247, G.248, H.250, R.303, Y.308, E.309, R.340 Chain T: D.58, R.67 Ligands: MG.19 11 PLIP interactions: 9 interactions with chain L, 2 Ligand-Ligand interactions Hydrogen bonds: L:E.139, L:Y.161, L:E.194, L:Q.199, L:N.245, L:G.246, L:E.309, Q.21, Q.21 Salt bridges: L:H.250, L:R.303 GLN.24: 17 residues within 4Å: Chain L: D.58, R.67 Chain N: E.139, Y.161, E.194, V.195, Q.199, N.245, G.246, S.247, G.248, H.250, R.303, Y.308, E.309, R.340 Ligands: MG.22 11 PLIP interactions: 8 interactions with chain N, 2 Ligand-Ligand interactions, 1 interactions with chain L Hydrogen bonds: N:E.139, N:Y.161, N:Q.199, N:N.245, N:G.246, N:E.309, Q.24, Q.24, L:R.67 Salt bridges: N:H.250, N:R.303 GLN.27: 17 residues within 4Å: Chain N: D.58, R.67 Chain O: E.139, Y.161, E.194, V.195, Q.199, N.245, G.246, S.247, G.248, H.250, R.303, Y.308, E.309, R.340 Ligands: MG.25 11 PLIP interactions: 8 interactions with chain O, 1 interactions with chain N, 2 Ligand-Ligand interactions Hydrogen bonds: O:E.139, O:Y.161, O:Q.199, O:N.245, O:G.246, O:E.309, N:R.67, Q.27, Q.27 Salt bridges: O:H.250, O:R.303 GLN.30: 17 residues within 4Å: Chain O: D.58, R.67 Chain R: E.139, Y.161, E.194, V.195, Q.199, N.245, G.246, S.247, G.248, H.250, R.303, Y.308, E.309, R.340 Ligands: MG.28 11 PLIP interactions: 9 interactions with chain R, 2 Ligand-Ligand interactions Hydrogen bonds: R:E.139, R:Y.161, R:E.194, R:Q.199, R:N.245, R:G.246, R:E.309, Q.30, Q.30 Salt bridges: R:H.250, R:R.303 GLN.33: 17 residues within 4Å: Chain R: D.58, R.67 Chain S: E.139, Y.161, E.194, V.195, Q.199, N.245, G.246, S.247, G.248, H.250, R.303, Y.308, E.309, R.340 Ligands: MG.31 10 PLIP interactions: 8 interactions with chain S, 2 Ligand-Ligand interactions Hydrogen bonds: S:E.139, S:Y.161, S:Q.199, S:N.245, S:G.246, S:E.309, Q.33, Q.33 Salt bridges: S:H.250, S:R.303 GLN.36: 16 residues within 4Å: Chain S: R.67 Chain T: E.139, Y.161, E.194, V.195, Q.199, N.245, G.246, S.247, G.248, H.250, R.303, Y.308, E.309, R.340 Ligands: MG.34 10 PLIP interactions: 7 interactions with chain T, 1 interactions with chain S, 2 Ligand-Ligand interactions Hydrogen bonds: T:E.139, T:Y.161, T:N.245, T:G.246, T:E.309, S:R.67, Q.36, Q.36 Salt bridges: T:H.250, T:R.303

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Travis, B.A. et al., Molecular dissection of the glutamine synthetase-GlnR nitrogen regulatory circuitry in Gram-positive bacteria. Nat Commun (2022)

Release Date

2022-06-29

Peptides

Glutamine synthetase: ABCFGHLNORST
Peptide from Glutamine synthetase repressor: DEIJKMPQUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

F
F

G
G

H
H

L
L

N
N

O
O

R
R

S
S

T
T

D
D

E
E

I
I

J
J

K
K

M
M

P
P

Q
Q

U
U

V
V

W
W

X
X

Glutamine synthetase

Peptide from Glutamine synthetase repressor

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