SMTL ID : 8g8p.1

F420-2/GTP(GDP) complex of F420-gamma glutamyl ligase (CofE) from Archaeoglobus fulgidus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-dimer

Ligands

2 x F42: COENZYME F420(Non-covalent)

F42.1: 24 residues within 4Å: Chain A: F.94, L.96, V.106, N.107, D.111, A.112, S.113, T.153, N.154, G.155, R.156, C.157, V.162 Chain B: R.187, L.189, E.190, V.191, T.192, R.236, E.240, D.241, V.242 Ligands: GTP.2, NA.6 33 PLIP interactions: 19 interactions with chain A, 14 interactions with chain B Hydrophobic interactions: A:F.94, A:V.106, A:V.162, B:L.189 Hydrogen bonds: A:N.107, A:A.112, A:S.113, A:T.153, A:G.155, B:R.187, B:E.190, B:V.191, B:T.192, B:T.192, B:R.236, B:E.240, B:D.241, B:V.242 Water bridges: A:V.106, A:V.106, A:D.111, A:T.153, A:T.153, A:N.154, A:G.155, A:R.156, A:G.161, A:G.161, B:R.236, B:R.236 pi-Stacking: A:F.94 pi-Cation interactions: B:R.236, B:R.236 F42.9: 24 residues within 4Å: Chain A: R.187, L.189, E.190, V.191, T.192, R.236, E.240, D.241, V.242 Chain B: F.94, L.96, V.106, N.107, D.111, A.112, S.113, T.153, N.154, G.155, R.156, C.157, V.162 Ligands: GTP.10, NA.14 31 PLIP interactions: 18 interactions with chain B, 13 interactions with chain A Hydrophobic interactions: B:F.94, B:V.106, B:V.162, A:L.189 Hydrogen bonds: B:N.107, B:A.112, B:S.113, B:T.153, B:G.155, A:R.187, A:E.190, A:V.191, A:T.192, A:R.236, A:E.240, A:V.242 Water bridges: B:V.106, B:V.106, B:D.111, B:T.153, B:N.154, B:G.155, B:R.156, B:G.161, B:G.161, A:T.192, A:R.236, A:R.236 pi-Stacking: B:F.94 pi-Cation interactions: A:R.236, A:R.236

2 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.2: 30 residues within 4Å: Chain A: L.13, P.14, L.15, I.16, C.41, S.42, T.43, V.44, K.47, D.111, S.113, N.114, D.152, T.153, M.208, G.209, E.210, G.211, G.212, D.213, G.214, I.215, P.216 Chain B: L.184 Ligands: F42.1, GDP.3, MN.4, MN.5, NA.6, MN.8 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:P.14, A:P.14, A:I.16, A:S.42, A:T.43, A:T.43, A:K.47, A:N.114, A:T.153, A:T.153, A:M.208, A:G.211, A:D.213, A:G.214, A:I.215 Water bridges: A:E.210, A:E.210, A:E.210, A:E.210, A:G.211 GTP.10: 30 residues within 4Å: Chain A: L.184 Chain B: L.13, P.14, L.15, I.16, C.41, S.42, T.43, V.44, K.47, D.111, S.113, N.114, D.152, T.153, M.208, G.209, E.210, G.211, G.212, D.213, G.214, I.215, P.216 Ligands: F42.9, GDP.11, MN.12, MN.13, NA.14, MN.16 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:P.14, B:P.14, B:I.16, B:S.42, B:T.43, B:T.43, B:K.47, B:N.114, B:D.152, B:T.153, B:T.153, B:M.208, B:G.211, B:D.213, B:G.214, B:I.215 Water bridges: B:S.113, B:S.113, B:G.211

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.3: 29 residues within 4Å: Chain A: L.13, P.14, L.15, I.16, C.41, S.42, T.43, V.44, K.47, D.111, S.113, N.114, T.151, D.152, T.153, M.208, G.209, E.210, G.211, G.212, D.213, G.214, I.215, P.216 Chain B: L.184 Ligands: GTP.2, MN.4, MN.5, MN.8 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:P.14, A:I.16, A:S.42, A:S.42, A:T.43, A:T.43, A:K.47, A:N.114, A:T.153, A:M.208, A:G.211, A:G.214, A:G.214, A:I.215 Water bridges: A:L.13, A:T.153, A:T.153, A:E.210, A:E.210, A:G.211 GDP.11: 29 residues within 4Å: Chain A: L.184 Chain B: L.13, P.14, L.15, I.16, C.41, S.42, T.43, V.44, K.47, D.111, S.113, N.114, T.151, D.152, T.153, M.208, G.209, E.210, G.211, G.212, D.213, G.214, I.215, P.216 Ligands: GTP.10, MN.12, MN.13, MN.16 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:P.14, B:I.16, B:S.42, B:T.43, B:T.43, B:K.47, B:N.114, B:D.152, B:D.152, B:T.153, B:T.153, B:M.208, B:G.211, B:G.214, B:G.214, B:I.215 Water bridges: B:L.13, B:S.113, B:T.151, B:G.211

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

MN.4: 4 residues within 4Å: Chain A: T.153, E.210 Ligands: GTP.2, GDP.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.153, A:E.210, H2O.1, H2O.1 MN.5: 6 residues within 4Å: Chain A: D.111, D.152 Ligands: GTP.2, GDP.3, NA.6, MN.8 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.111, A:D.152, H2O.1, H2O.1, H2O.2 MN.8: 8 residues within 4Å: Chain A: S.42, G.109, D.111, D.152 Ligands: GTP.2, GDP.3, MN.5, NA.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.111, A:D.152, A:D.152, H2O.1, H2O.2 MN.12: 4 residues within 4Å: Chain B: T.153, E.210 Ligands: GTP.10, GDP.11 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.153, B:E.210, H2O.5, H2O.6 MN.13: 6 residues within 4Å: Chain B: D.111, D.152 Ligands: GTP.10, GDP.11, NA.14, MN.16 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.111, B:D.152, H2O.5, H2O.6, H2O.7 MN.16: 8 residues within 4Å: Chain B: S.42, G.109, D.111, D.152 Ligands: GTP.10, GDP.11, MN.13, NA.14 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.111, B:D.152, B:D.152, H2O.6, H2O.7

2 x NA: SODIUM ION(Non-functional Binders)

NA.6: 7 residues within 4Å: Chain A: G.109, D.111, T.153 Ligands: F42.1, GTP.2, MN.5, MN.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.111 NA.14: 7 residues within 4Å: Chain B: G.109, D.111, T.153 Ligands: F42.9, GTP.10, MN.13, MN.16 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.153

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

SO4.7: 4 residues within 4Å: Chain A: R.63, E.86, E.87, V.88 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.87, A:V.88 Salt bridges: A:R.63 SO4.15: 4 residues within 4Å: Chain B: R.63, E.86, E.87, V.88 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.88 Salt bridges: B:R.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bashiri, G. et al., Poly-gamma-glutamylation of biomolecules. Nat Commun (2024)

Release Date

2024-02-28

Peptides

Coenzyme F420:L-glutamate ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
AAA

Coenzyme F420:L-glutamate ligase

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