SMTL ID : 7tdv.1

Crystal structure of S. aureus glutamine synthetase in Met-Sox-P/ADP transition state complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.92 Å

Oligo State

homo-12-mer

Ligands

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

ADP.1: 26 residues within 4Å: Chain A: N.133, L.134, G.135, P.136, E.137, E.189, E.201, D.203, F.204, K.205, Y.206, N.252, V.253, S.254, F.256, N.261, R.321, R.326, L.333, S.334, T.335, R.336, E.338 Ligands: P3S.2, MG.3, MG.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.135, A:F.204, A:F.204, A:S.254, A:N.261, A:L.333, A:R.336 Salt bridges: A:R.321, A:R.326 ADP.5: 26 residues within 4Å: Chain B: N.133, L.134, G.135, P.136, E.137, E.189, E.201, D.203, F.204, K.205, Y.206, N.252, V.253, S.254, F.256, N.261, R.321, R.326, L.333, S.334, T.335, R.336, E.338 Ligands: P3S.6, MG.8, MG.9 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.135, B:F.204, B:F.204, B:Y.206, B:S.254, B:N.261, B:L.333 Water bridges: B:D.203, B:R.321, B:R.321, A:M.56 Salt bridges: B:R.321, B:R.326, B:R.336, B:R.336 ADP.12: 25 residues within 4Å: Chain C: N.133, L.134, G.135, E.137, E.189, E.201, D.203, F.204, K.205, Y.206, N.252, V.253, S.254, F.256, N.261, R.321, R.326, L.333, S.334, T.335, R.336, E.338 Ligands: P3S.13, MG.14, MG.15 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:E.189, C:E.189, C:D.203, C:F.204, C:Y.206, C:N.252, C:S.254, C:N.261, C:S.334, C:R.336 Salt bridges: C:R.321, C:R.326 ADP.17: 26 residues within 4Å: Chain D: N.133, L.134, G.135, P.136, E.137, E.189, E.201, D.203, F.204, K.205, Y.206, N.252, V.253, S.254, F.256, N.261, R.321, R.326, L.333, S.334, T.335, R.336, E.338 Ligands: P3S.18, MG.19, MG.20 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:G.135, D:F.204, D:F.204, D:S.254, D:S.254, D:N.261, D:R.336 Salt bridges: D:R.321, D:R.326 ADP.23: 25 residues within 4Å: Chain E: N.133, L.134, G.135, E.137, E.189, E.201, D.203, F.204, K.205, Y.206, N.252, V.253, S.254, F.256, N.261, R.321, R.326, L.333, S.334, T.335, R.336, E.338 Ligands: P3S.24, MG.25, MG.26 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:G.135, E:E.189, E:E.201, E:Y.206, E:S.254, E:N.261, E:L.333, E:R.336 Salt bridges: E:R.321, E:R.326, E:R.336 pi-Stacking: E:Y.206, E:Y.206 ADP.30: 25 residues within 4Å: Chain F: N.133, L.134, G.135, E.137, E.189, E.201, D.203, F.204, K.205, Y.206, N.252, V.253, S.254, F.256, N.261, R.321, R.326, L.333, S.334, T.335, R.336, E.338 Ligands: P3S.31, MG.32, MG.33 17 PLIP interactions: 16 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:G.135, F:E.189, F:E.189, F:E.201, F:Y.206, F:S.254, F:N.261, F:L.333, F:R.336 Water bridges: F:D.203, F:N.252, F:N.252, E:M.56 Salt bridges: F:R.321, F:R.326 pi-Stacking: F:Y.206, F:Y.206 ADP.35: 26 residues within 4Å: Chain G: N.133, L.134, G.135, P.136, E.137, E.189, E.201, D.203, F.204, K.205, Y.206, N.252, V.253, S.254, F.256, N.261, R.321, R.326, L.333, S.334, T.335, R.336, E.338 Ligands: P3S.36, MG.37, MG.38 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:G.135, G:E.189, G:F.204, G:F.204, G:S.254, G:N.261, G:L.333, G:R.336 Salt bridges: G:R.321, G:R.326 ADP.39: 26 residues within 4Å: Chain H: N.133, L.134, G.135, P.136, E.137, E.189, E.201, D.203, F.204, K.205, Y.206, N.252, V.253, S.254, F.256, N.261, R.321, R.326, L.333, S.334, T.335, R.336, E.338 Ligands: P3S.40, MG.42, MG.43 15 PLIP interactions: 14 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:G.135, H:F.204, H:F.204, H:Y.206, H:S.254, H:N.261, H:L.333 Water bridges: H:D.203, H:R.321, H:R.321, G:M.56 Salt bridges: H:R.321, H:R.326, H:R.336, H:R.336 ADP.46: 25 residues within 4Å: Chain I: N.133, L.134, G.135, E.137, E.189, E.201, D.203, F.204, K.205, Y.206, N.252, V.253, S.254, F.256, N.261, R.321, R.326, L.333, S.334, T.335, R.336, E.338 Ligands: P3S.47, MG.48, MG.49 12 PLIP interactions: 12 interactions with chain I Hydrogen bonds: I:E.189, I:E.189, I:E.189, I:F.204, I:Y.206, I:N.252, I:S.254, I:N.261, I:S.334, I:R.336 Salt bridges: I:R.321, I:R.326 ADP.51: 26 residues within 4Å: Chain J: N.133, L.134, G.135, P.136, E.137, E.189, E.201, D.203, F.204, K.205, Y.206, N.252, V.253, S.254, F.256, N.261, R.321, R.326, L.333, S.334, T.335, R.336, E.338 Ligands: P3S.52, MG.53, MG.54 9 PLIP interactions: 9 interactions with chain J Hydrogen bonds: J:G.135, J:F.204, J:F.204, J:S.254, J:S.254, J:N.261, J:R.336 Salt bridges: J:R.321, J:R.326 ADP.57: 25 residues within 4Å: Chain K: N.133, L.134, G.135, E.137, E.189, E.201, D.203, F.204, K.205, Y.206, N.252, V.253, S.254, F.256, N.261, R.321, R.326, L.333, S.334, T.335, R.336, E.338 Ligands: P3S.58, MG.59, MG.60 15 PLIP interactions: 15 interactions with chain K Hydrogen bonds: K:G.135, K:E.189, K:D.203, K:Y.206, K:S.254, K:N.261, K:L.333, K:R.336 Water bridges: K:H.192, K:D.203 Salt bridges: K:R.321, K:R.326, K:R.336 pi-Stacking: K:Y.206, K:Y.206 ADP.64: 25 residues within 4Å: Chain L: N.133, L.134, G.135, E.137, E.189, E.201, D.203, F.204, K.205, Y.206, N.252, V.253, S.254, F.256, N.261, R.321, R.326, L.333, S.334, T.335, R.336, E.338 Ligands: P3S.65, MG.66, MG.67 17 PLIP interactions: 16 interactions with chain L, 1 interactions with chain K Hydrogen bonds: L:G.135, L:E.189, L:E.189, L:E.189, L:Y.206, L:S.254, L:N.261, L:L.333, L:R.336 Water bridges: L:D.203, L:N.252, L:N.252, K:M.56 Salt bridges: L:R.321, L:R.326 pi-Stacking: L:Y.206, L:Y.206

12 x P3S: L-METHIONINE-S-SULFOXIMINE PHOSPHATE(Non-covalent)(Covalent)

P3S.2: 23 residues within 4Å: Chain A: E.137, E.139, Y.161, E.194, V.195, E.201, N.245, G.246, S.247, G.248, H.250, R.303, Y.308, E.309, A.310, R.321, E.338, R.340 Chain D: D.58, S.61 Ligands: ADP.1, MG.3, MG.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:E.137, A:E.139, A:E.139, A:G.248, A:H.250, A:R.321, A:R.340, A:R.340 Salt bridges: A:H.250, A:R.303 P3S.6: 25 residues within 4Å: Chain A: D.58, S.61 Chain B: E.137, E.139, Y.161, E.194, V.195, Q.199, E.201, N.245, G.246, S.247, G.248, H.250, R.303, Y.308, E.309, A.310, R.321, E.338, R.340 Ligands: ADP.5, MG.7, MG.8, MG.9 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:E.309 Hydrogen bonds: B:Q.199, B:G.246, B:R.321, B:R.340, A:D.58 Salt bridges: B:H.250, B:R.303 P3S.13: 23 residues within 4Å: Chain C: E.137, E.139, Y.161, E.194, V.195, E.201, N.245, G.246, S.247, G.248, H.250, R.303, Y.308, E.309, A.310, R.321, E.338, R.340 Chain F: D.58, S.61 Ligands: ADP.12, MG.14, MG.15 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:E.309 Hydrogen bonds: C:E.139, C:E.194, C:G.246, C:G.248, C:H.250, C:R.321, C:R.340, C:R.340 Salt bridges: C:H.250, C:R.303 P3S.18: 23 residues within 4Å: Chain C: D.58, S.61 Chain D: E.137, E.139, Y.161, E.194, V.195, E.201, N.245, G.246, S.247, G.248, H.250, R.303, Y.308, E.309, A.310, R.321, E.338, R.340 Ligands: ADP.17, MG.19, MG.20 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:Y.161, D:N.245, D:G.248, D:H.250, D:R.321, D:R.340, D:R.340 Salt bridges: D:H.250, D:R.303 P3S.24: 26 residues within 4Å: Chain B: D.58, S.61 Chain E: E.137, E.139, Y.161, E.194, V.195, Q.199, E.201, N.245, G.246, S.247, G.248, H.250, R.303, Y.308, E.309, A.310, R.321, R.326, E.338, R.340 Ligands: ADP.23, MG.25, MG.26, MG.28 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:E.309 Hydrogen bonds: E:E.137, E:G.246, E:H.250, E:R.321, E:R.326, E:R.340 Salt bridges: E:H.250, E:R.303 P3S.31: 24 residues within 4Å: Chain E: D.58, S.61 Chain F: E.137, E.139, Y.161, E.194, V.195, Q.199, E.201, N.245, G.246, S.247, G.248, H.250, R.303, Y.308, E.309, A.310, R.321, E.338, R.340 Ligands: ADP.30, MG.32, MG.33 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:E.137, F:E.139, F:E.194, F:G.246, F:G.248, F:H.250, F:R.321, F:R.340 Water bridges: F:N.245, F:G.246 Salt bridges: F:H.250, F:R.303, F:R.340 P3S.36: 23 residues within 4Å: Chain G: E.137, E.139, Y.161, E.194, V.195, E.201, N.245, G.246, S.247, G.248, H.250, R.303, Y.308, E.309, A.310, R.321, E.338, R.340 Chain J: D.58, S.61 Ligands: ADP.35, MG.37, MG.38 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:E.137, G:E.139, G:E.194, G:G.248, G:R.321, G:R.340, G:R.340 Salt bridges: G:H.250, G:R.303 P3S.40: 25 residues within 4Å: Chain G: D.58, S.61 Chain H: E.137, E.139, Y.161, E.194, V.195, Q.199, E.201, N.245, G.246, S.247, G.248, H.250, R.303, Y.308, E.309, A.310, R.321, E.338, R.340 Ligands: ADP.39, MG.41, MG.42, MG.43 7 PLIP interactions: 7 interactions with chain H Hydrophobic interactions: H:E.309 Hydrogen bonds: H:Q.199, H:G.246, H:R.321, H:R.340 Salt bridges: H:H.250, H:R.303 P3S.47: 23 residues within 4Å: Chain I: E.137, E.139, Y.161, E.194, V.195, E.201, N.245, G.246, S.247, G.248, H.250, R.303, Y.308, E.309, A.310, R.321, E.338, R.340 Chain L: D.58, S.61 Ligands: ADP.46, MG.48, MG.49 8 PLIP interactions: 8 interactions with chain I Hydrophobic interactions: I:E.309 Hydrogen bonds: I:G.246, I:G.248, I:R.321, I:R.340, I:R.340 Salt bridges: I:H.250, I:R.303 P3S.52: 23 residues within 4Å: Chain I: D.58, S.61 Chain J: E.137, E.139, Y.161, E.194, V.195, E.201, N.245, G.246, S.247, G.248, H.250, R.303, Y.308, E.309, A.310, R.321, E.338, R.340 Ligands: ADP.51, MG.53, MG.54 8 PLIP interactions: 7 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:N.245, J:G.248, J:R.321, J:R.340, J:R.340, I:D.58 Salt bridges: J:H.250, J:R.303 P3S.58: 26 residues within 4Å: Chain H: D.58, S.61 Chain K: E.137, E.139, Y.161, E.194, V.195, Q.199, E.201, N.245, G.246, S.247, G.248, H.250, R.303, Y.308, E.309, A.310, R.321, R.326, E.338, R.340 Ligands: ADP.57, MG.59, MG.60, MG.62 8 PLIP interactions: 8 interactions with chain K Hydrophobic interactions: K:E.309 Hydrogen bonds: K:E.137, K:G.246, K:R.321, K:R.326, K:R.340 Salt bridges: K:H.250, K:R.303 P3S.65: 24 residues within 4Å: Chain K: D.58, S.61 Chain L: E.137, E.139, Y.161, E.194, V.195, Q.199, E.201, N.245, G.246, S.247, G.248, H.250, R.303, Y.308, E.309, A.310, R.321, E.338, R.340 Ligands: ADP.64, MG.66, MG.67 11 PLIP interactions: 10 interactions with chain L, 1 interactions with chain K Hydrogen bonds: L:E.137, L:G.246, L:G.248, L:R.321, L:R.340, K:D.58 Water bridges: L:N.245, L:G.246 Salt bridges: L:H.250, L:R.303, L:R.340

42 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: E.137, E.201, D.203 Ligands: ADP.1, P3S.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.137, A:E.201 MG.4: 7 residues within 4Å: Chain A: E.137, H.250, R.326, E.338, R.340 Ligands: ADP.1, P3S.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.137, A:E.137, A:H.250, A:E.338 MG.7: 6 residues within 4Å: Chain B: E.137, E.139, E.194, E.201 Ligands: P3S.6, MG.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.139, B:E.194, B:E.201 MG.8: 7 residues within 4Å: Chain B: E.137, E.201, D.203 Ligands: ADP.5, P3S.6, MG.7, MG.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.137, B:E.201, H2O.3 MG.9: 6 residues within 4Å: Chain B: E.137, H.250, E.338 Ligands: ADP.5, P3S.6, MG.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.137, B:E.137, B:H.250, B:E.338 MG.10: 2 residues within 4Å: Chain B: D.265, E.274 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.265 MG.11: 1 residues within 4Å: Chain B: E.54 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.54, B:E.54 MG.14: 6 residues within 4Å: Chain C: E.137, H.192, E.201, D.203 Ligands: ADP.12, P3S.13 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.137, C:E.201 MG.15: 7 residues within 4Å: Chain C: E.137, H.250, R.326, E.338, R.340 Ligands: ADP.12, P3S.13 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.137, C:H.250, C:E.338 MG.16: 2 residues within 4Å: Chain C: S.60, E.63 No protein-ligand interaction detected (PLIP) MG.19: 5 residues within 4Å: Chain D: E.137, E.201, D.203 Ligands: ADP.17, P3S.18 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.137, D:E.201 MG.20: 6 residues within 4Å: Chain D: E.137, H.250, E.338, R.340 Ligands: ADP.17, P3S.18 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.137, D:E.137, D:H.250, D:E.338 MG.21: 2 residues within 4Å: Chain D: S.60, E.63 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.60 MG.22: 2 residues within 4Å: Chain D: P.86, W.87 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:P.86 MG.25: 5 residues within 4Å: Chain E: E.137, E.201, D.203 Ligands: ADP.23, P3S.24 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.137, E:E.201, H2O.8 MG.26: 6 residues within 4Å: Chain E: E.137, H.250, R.326, E.338 Ligands: ADP.23, P3S.24 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:E.137, E:E.137, E:H.250, E:E.338 MG.27: 2 residues within 4Å: Chain E: D.52, E.54 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.52, E:E.54 MG.28: 4 residues within 4Å: Chain E: E.139, E.194, E.201 Ligands: P3S.24 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.139, E:E.194, E:E.201 MG.29: 3 residues within 4Å: Chain E: P.86, E.180, D.183 No protein-ligand interaction detected (PLIP) MG.32: 5 residues within 4Å: Chain F: E.137, E.201, D.203 Ligands: ADP.30, P3S.31 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:E.137, F:E.201 MG.33: 5 residues within 4Å: Chain F: E.137, H.250, E.338 Ligands: ADP.30, P3S.31 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:E.137, F:E.137, F:H.250, F:E.338 MG.37: 5 residues within 4Å: Chain G: E.137, E.201, D.203 Ligands: ADP.35, P3S.36 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:E.137, G:E.201 MG.38: 7 residues within 4Å: Chain G: E.137, H.250, R.326, E.338, R.340 Ligands: ADP.35, P3S.36 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:E.137, G:E.137, G:H.250, G:E.338 MG.41: 6 residues within 4Å: Chain H: E.137, E.139, E.194, E.201 Ligands: P3S.40, MG.42 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.139, H:E.194, H:E.201 MG.42: 7 residues within 4Å: Chain H: E.137, E.201, D.203 Ligands: ADP.39, P3S.40, MG.41, MG.43 3 PLIP interactions: 2 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.137, H:E.201, H2O.15 MG.43: 6 residues within 4Å: Chain H: E.137, H.250, E.338 Ligands: ADP.39, P3S.40, MG.42 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:E.137, H:E.137, H:H.250, H:E.338 MG.44: 2 residues within 4Å: Chain H: D.265, E.274 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.265 MG.45: 1 residues within 4Å: Chain H: E.54 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:E.54, H:E.54 MG.48: 6 residues within 4Å: Chain I: E.137, H.192, E.201, D.203 Ligands: ADP.46, P3S.47 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:E.137, I:E.201 MG.49: 7 residues within 4Å: Chain I: E.137, H.250, R.326, E.338, R.340 Ligands: ADP.46, P3S.47 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:E.137, I:H.250, I:E.338 MG.50: 2 residues within 4Å: Chain I: S.60, E.63 No protein-ligand interaction detected (PLIP) MG.53: 5 residues within 4Å: Chain J: E.137, E.201, D.203 Ligands: ADP.51, P3S.52 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:E.137, J:E.201 MG.54: 6 residues within 4Å: Chain J: E.137, H.250, E.338, R.340 Ligands: ADP.51, P3S.52 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:E.137, J:E.137, J:H.250, J:E.338 MG.55: 2 residues within 4Å: Chain J: S.60, E.63 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:S.60 MG.56: 2 residues within 4Å: Chain J: P.86, W.87 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:P.86 MG.59: 5 residues within 4Å: Chain K: E.137, E.201, D.203 Ligands: ADP.57, P3S.58 3 PLIP interactions: 2 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:E.137, K:E.201, H2O.20 MG.60: 6 residues within 4Å: Chain K: E.137, H.250, R.326, E.338 Ligands: ADP.57, P3S.58 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:E.137, K:E.137, K:H.250, K:E.338 MG.61: 2 residues within 4Å: Chain K: D.52, E.54 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.52, K:E.54 MG.62: 4 residues within 4Å: Chain K: E.139, E.194, E.201 Ligands: P3S.58 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:E.139, K:E.194, K:E.201 MG.63: 3 residues within 4Å: Chain K: P.86, E.180, D.183 No protein-ligand interaction detected (PLIP) MG.66: 5 residues within 4Å: Chain L: E.137, E.201, D.203 Ligands: ADP.64, P3S.65 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:E.137, L:E.201 MG.67: 5 residues within 4Å: Chain L: E.137, H.250, E.338 Ligands: ADP.64, P3S.65 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:E.137, L:E.137, L:H.250, L:E.338

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.34: 3 residues within 4Å: Chain F: Y.398, L.401, R.405 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:R.405 SO4.68: 3 residues within 4Å: Chain L: Y.398, L.401, R.405 1 PLIP interactions: 1 interactions with chain L Salt bridges: L:R.405

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: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

D
E

E
B

F
H

G
A

H
C

I
D

J
E

K
B

L
H

Glutamine synthetase