SMTL ID : 7uld.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

2 x CO3: CARBONATE ION(Non-functional Binders)

CO3.1: 5 residues within 4Å: Chain A: R.187, L.189, E.190, V.191, T.192 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.192 Water bridges: B:S.113 CO3.9: 5 residues within 4Å: Chain B: R.187, L.189, E.190, V.191, T.192 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:S.113 Hydrogen bonds: B:T.192, B:T.192

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

MN.2: 3 residues within 4Å: Chain A: T.153, E.210 Ligands: GTP.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.153, A:E.210, H2O.1 MN.3: 4 residues within 4Å: Chain A: G.109, D.111, D.152 Ligands: GTP.5 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.111, A:D.152, H2O.1, H2O.2, H2O.6 MN.10: 3 residues within 4Å: Chain B: T.153, E.210 Ligands: GTP.13 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.153, B:E.210, H2O.9 MN.11: 4 residues within 4Å: Chain B: G.109, D.111, D.152 Ligands: GTP.13 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.111, B:D.152, H2O.9, H2O.10, H2O.14

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

NA.4: 6 residues within 4Å: Chain A: F.101, N.103, C.105, G.109, D.152, N.154 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.103, A:N.154, A:N.154 Water bridges: A:V.106 NA.12: 6 residues within 4Å: Chain B: F.101, N.103, C.105, G.109, D.152, N.154 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.103, B:N.154, B:N.154 Water bridges: B:V.106

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

GTP.5: 26 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: MN.2, MN.3 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: 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:G.214, A:I.215 Water bridges: A:L.13, A:S.113, A:S.113, A:S.113 GTP.13: 26 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: MN.10, MN.11 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: 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:G.214, B:I.215 Water bridges: B:L.13, B:S.113, B:S.113, B:S.113

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

SO4.6: 3 residues within 4Å: Chain A: R.63, E.87, V.88 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.88, A:V.88 Salt bridges: A:R.63 SO4.7: 5 residues within 4Å: Chain A: K.98, R.236, S.237, E.238, R.244 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.238, A:E.238 Water bridges: A:K.98, A:S.237, A:E.239 Salt bridges: A:K.98, A:R.244 SO4.8: 1 residues within 4Å: Chain A: E.188 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.188 SO4.14: 3 residues within 4Å: Chain B: R.63, E.87, V.88 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.88, B:V.88 Salt bridges: B:R.63 SO4.15: 5 residues within 4Å: Chain B: K.98, R.236, S.237, E.238, R.244 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.238 Water bridges: B:K.98, B:S.237, B:E.239 Salt bridges: B:K.98, B:R.244 SO4.16: 1 residues within 4Å: Chain B: E.188 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.188

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bashiri, G. et al., A Universal Mechanism for Poly-glutamylation. To Be Published

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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