SMTL ID : 8wwu.1

1-naphthylamine GS in complex with AMP PNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

6 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 27 residues within 4Å: Chain A: K.173, C.174, G.175, I.176, E.177, R.244, E.256, T.258, F.259, D.260, V.261, H.306, H.308, Q.309, S.310, N.319, K.378, R.383, P.391, A.392, S.393, R.394, E.396, R.398 Chain E: K.66 Ligands: MN.3, MG.4 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:G.175, A:R.244, A:F.259, A:S.310, A:K.378, A:R.383, A:R.383, A:A.392, A:R.394, A:R.398, A:R.398 Water bridges: A:E.177, A:E.177, A:R.244, A:S.245, A:N.319 Salt bridges: A:R.244, A:H.308, E:K.66 pi-Cation interactions: A:R.394 ANP.5: 27 residues within 4Å: Chain B: K.173, C.174, G.175, I.176, E.177, R.244, E.256, T.258, F.259, D.260, V.261, H.306, H.308, Q.309, S.310, N.319, K.378, R.383, P.391, A.392, S.393, R.394, E.396, R.398 Ligands: MN.6, MN.7, MG.8 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:G.175, B:R.244, B:F.259, B:S.310, B:K.378, B:R.383, B:R.383, B:A.392, B:R.394, B:R.398, B:R.398 Water bridges: B:E.177, B:E.177, B:E.177, B:R.244, B:E.247, B:E.247, B:E.256 Salt bridges: B:R.244, B:H.308 pi-Cation interactions: B:R.394 ANP.9: 27 residues within 4Å: Chain A: K.66 Chain C: K.173, C.174, G.175, I.176, E.177, R.244, E.256, F.259, D.260, V.261, H.306, H.308, Q.309, S.310, N.319, K.378, R.383, P.391, A.392, S.393, R.394, E.396, R.398 Ligands: MN.10, MN.11, MG.12 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:G.175, C:E.177, C:F.259, C:S.310, C:K.378, C:K.378, C:R.383, C:R.383, C:S.393, C:R.394, C:R.398 Water bridges: C:R.244, C:R.244, C:R.398 Salt bridges: C:R.244, C:H.308, A:K.66 ANP.13: 27 residues within 4Å: Chain B: K.66 Chain D: K.173, C.174, G.175, I.176, E.177, R.244, E.256, F.259, D.260, V.261, H.306, H.308, Q.309, S.310, N.319, K.378, R.383, P.391, A.392, S.393, R.394, E.396, R.398 Ligands: MN.14, MN.15, MG.16 19 PLIP interactions: 16 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:G.175, D:S.310, D:K.378, D:R.383, D:R.383, D:A.392, D:R.394, D:R.394, D:R.398 Water bridges: D:E.177, D:R.244, D:E.256, D:R.398, B:K.66, B:K.66 Salt bridges: D:R.244, D:H.308, B:K.66 pi-Cation interactions: D:R.394 ANP.17: 27 residues within 4Å: Chain D: K.66 Chain E: K.173, C.174, G.175, I.176, E.177, R.244, E.256, T.258, F.259, D.260, V.261, H.308, Q.309, S.310, N.319, K.378, R.383, P.391, A.392, S.393, R.394, E.396, R.398 Ligands: MN.18, MN.19, MG.20 21 PLIP interactions: 18 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:G.175, E:E.177, E:F.259, E:S.310, E:K.378, E:R.383, E:R.383, E:S.393, E:R.394, E:R.398 Water bridges: E:E.177, E:R.244, E:R.394, E:R.394, E:R.394, D:K.66, D:A.84 Salt bridges: E:R.244, E:H.308, D:K.66 pi-Cation interactions: E:R.394 ANP.21: 28 residues within 4Å: Chain C: K.66 Chain F: K.173, C.174, G.175, I.176, E.177, R.244, E.256, T.258, F.259, D.260, V.261, H.306, H.308, Q.309, S.310, N.319, K.378, R.383, P.391, A.392, S.393, R.394, E.396, R.398 Ligands: MN.22, MN.23, MG.24 14 PLIP interactions: 12 interactions with chain F, 2 interactions with chain C Hydrogen bonds: F:G.175, F:F.259, F:S.310, F:R.383, F:R.383, F:S.393, F:R.394, F:R.398 Water bridges: F:R.394, C:T.116 Salt bridges: F:R.244, F:H.308, C:K.66 pi-Cation interactions: F:R.394

12 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 3 residues within 4Å: Chain A: E.179, E.249, E.256 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.179, A:E.249, A:E.256, H2O.2 MN.3: 7 residues within 4Å: Chain A: E.177, H.306, H.308, E.396, R.398 Ligands: ANP.1, MG.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.177, A:E.177, A:H.306, A:E.396 MN.6: 4 residues within 4Å: Chain B: E.179, E.249, E.256 Ligands: ANP.5 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.179, B:E.249, B:E.256, H2O.13, H2O.14 MN.7: 6 residues within 4Å: Chain B: E.177, H.306, H.308, E.396, R.398 Ligands: ANP.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.177, B:E.177, B:H.306, B:E.396 MN.10: 5 residues within 4Å: Chain C: E.177, E.179, E.249, E.256 Ligands: ANP.9 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.179, C:E.249, C:E.256, H2O.34 MN.11: 7 residues within 4Å: Chain C: E.177, H.306, H.308, E.396, R.398 Ligands: ANP.9, MG.12 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.177, C:E.177, C:H.306, C:E.396 MN.14: 4 residues within 4Å: Chain D: E.179, E.249, E.256 Ligands: ANP.13 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.179, D:E.249, D:E.256, H2O.42 MN.15: 6 residues within 4Å: Chain D: E.177, H.306, H.308, E.396, R.398 Ligands: ANP.13 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.177, D:E.177, D:H.306, D:E.396 MN.18: 5 residues within 4Å: Chain E: E.179, E.249, E.256 Ligands: ANP.17, MG.20 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.179, E:E.249, E:E.256 MN.19: 7 residues within 4Å: Chain E: E.177, H.306, H.308, E.396, R.398 Ligands: ANP.17, MG.20 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:E.177, E:E.177, E:H.306, E:E.396 MN.22: 6 residues within 4Å: Chain F: E.177, E.179, E.249, E.256 Ligands: ANP.21, MG.24 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.179, F:E.249, F:E.256, H2O.74 MN.23: 6 residues within 4Å: Chain F: E.177, H.306, H.308, E.396, R.398 Ligands: ANP.21 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:E.177, F:E.177, F:H.306, F:E.396

6 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: E.177, E.256 Ligands: ANP.1, MN.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.177, A:E.256, H2O.2 MG.8: 3 residues within 4Å: Chain B: E.177, E.256 Ligands: ANP.5 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.177, B:E.256, H2O.14 MG.12: 4 residues within 4Å: Chain C: E.177, E.256 Ligands: ANP.9, MN.11 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.256, H2O.27 MG.16: 4 residues within 4Å: Chain D: E.177, E.247, E.256 Ligands: ANP.13 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.177, D:E.256 MG.20: 5 residues within 4Å: Chain E: E.177, E.256 Ligands: ANP.17, MN.18, MN.19 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.177, E:E.256, H2O.55 MG.24: 5 residues within 4Å: Chain F: E.177, E.247, E.256 Ligands: ANP.21, MN.22 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:E.177, F:E.256

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, S.T. et al., Discovery of the 1-naphthylamine biodegradation pathway reveals a glutamine synthetase-like protein that catalyzes 1-naphthylamine glutamylation. To Be Published

Release Date

2024-01-03

Peptides

Glutamine synthetase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Glutamine synthetase

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