SMTL ID : 7ulf.1

l-glutamate/GTP complex of F420-gamma glutamyl ligase (CofE) from Archaeoglobus fulgidus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

homo-dimer

Ligands

2 x GGL: GAMMA-L-GLUTAMIC ACID(Non-covalent)

GGL.1: 9 residues within 4Å: Chain A: D.111, A.112, S.113 Chain B: R.187, L.189, E.190, V.191, T.192 Ligands: GTP.2 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:D.111, A:A.112, A:S.113, A:S.113, B:R.187, B:E.190, B:V.191, B:T.192, B:T.192 Hydrophobic interactions: B:L.189, B:V.191 GGL.5: 9 residues within 4Å: Chain A: R.187, L.189, E.190, V.191, T.192 Chain B: D.111, A.112, S.113 Ligands: GTP.6 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:D.111, B:A.112, B:S.113, B:S.113, A:R.187, A:E.190, A:V.191, A:T.192 Hydrophobic interactions: A:L.189, A:V.191 Water bridges: A:T.192

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

GTP.2: 27 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: GGL.1, MN.3, MN.4 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: 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:M.208, A:G.211, A:D.213, A:G.214, A:G.214, A:I.215 Water bridges: A:L.13, A:S.113, A:S.113, A:G.211 GTP.6: 27 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: GGL.5, MN.7, MN.8 18 PLIP interactions: 18 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:T.153, B:M.208, B:G.211, B:D.213, B:G.214, B:G.214, B:I.215 Water bridges: B:L.13, B:S.113, B:S.113, B:G.211

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

MN.3: 3 residues within 4Å: Chain A: T.153, E.210 Ligands: GTP.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.153, A:E.210, H2O.1 MN.4: 4 residues within 4Å: Chain A: G.109, D.111, D.152 Ligands: GTP.2 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.3 MN.7: 3 residues within 4Å: Chain B: T.153, E.210 Ligands: GTP.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.153, B:E.210, H2O.4 MN.8: 4 residues within 4Å: Chain B: G.109, D.111, D.152 Ligands: GTP.6 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.111, B:D.152, H2O.4, H2O.5, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2023-04-12

Peptides

Coenzyme F420:L-glutamate ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Coenzyme F420:L-glutamate ligase

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