SMTL ID : 2phn.1

Crystal structure of an amide bond forming F420-gamma glutamyl ligase from Archaeoglobus fulgidus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 3 residues within 4Å: Chain A: T.154, E.211 Ligands: GDP.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.154, A:E.211, H2O.2, H2O.4 MN.2: 3 residues within 4Å: Chain A: D.112, D.153 Ligands: GDP.6 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.112, A:D.153, H2O.1, H2O.3, H2O.4 MN.12: 3 residues within 4Å: Chain B: T.154, E.211 Ligands: GDP.15 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.154, B:E.211, H2O.14, H2O.15 MN.13: 3 residues within 4Å: Chain B: D.112, D.153 Ligands: GDP.15 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.112, B:D.153, H2O.14, H2O.15, H2O.19

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 5 residues within 4Å: Chain A: F.9, V.31, R.32, R.222 Chain B: R.5 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.9, A:V.31 Hydrogen bonds: A:R.32, A:R.32 Salt bridges: A:R.222, B:R.5 Water bridges: B:R.5 ACT.4: 7 residues within 4Å: Chain A: F.95 Chain B: R.237, E.241, D.242, V.243, I.244 Ligands: ACT.5 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:F.95 Hydrogen bonds: B:D.242, B:V.243, B:I.244 Water bridges: B:R.237, B:R.237 Salt bridges: B:R.237 ACT.5: 7 residues within 4Å: Chain A: V.107, G.156, R.157, C.158 Chain B: F.159, I.244 Ligands: ACT.4 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.156 Water bridges: A:R.157, B:R.237 Hydrophobic interactions: B:F.159 ACT.14: 5 residues within 4Å: Chain B: F.95, V.107, G.156, R.157, C.158 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.95 Hydrogen bonds: B:R.157 Water bridges: B:G.156

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

GDP.6: 27 residues within 4Å: Chain A: L.14, P.15, L.16, I.17, C.42, S.43, T.44, V.45, K.48, D.112, N.115, T.152, D.153, T.154, M.209, G.210, E.211, G.212, G.213, D.214, G.215, I.216, P.217 Chain B: L.185 Ligands: MN.1, MN.2, GOL.11 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:P.15, A:I.17, A:S.43, A:T.44, A:T.44, A:K.48, A:N.115, A:T.154, A:M.209, A:G.212, A:D.214, A:G.215, A:G.215, A:I.216 Water bridges: A:L.14, A:N.206, A:D.214 GDP.15: 26 residues within 4Å: Chain A: L.185 Chain B: L.14, P.15, L.16, I.17, C.42, S.43, T.44, V.45, K.48, D.112, N.115, T.152, D.153, T.154, M.209, G.210, E.211, G.212, G.213, D.214, G.215, I.216, P.217 Ligands: MN.12, MN.13 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:P.15, B:I.17, B:S.43, B:T.44, B:T.44, B:K.48, B:N.115, B:T.154, B:M.209, B:G.212, B:D.214, B:G.215, B:G.215, B:I.216 Water bridges: B:L.14, B:T.44, B:S.114, B:T.152

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 3 residues within 4Å: Chain A: K.177, L.224, N.225 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.177, A:N.225 EDO.8: 5 residues within 4Å: Chain A: L.207 Chain B: K.177, L.224, N.225, V.226 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.177, B:N.225 EDO.9: 5 residues within 4Å: Chain A: L.91, F.93, C.251 Chain B: V.243, C.247 1 PLIP interactions: 1 interactions with chain A Water bridges: A:F.93 EDO.10: 9 residues within 4Å: Chain A: R.157, V.164, F.166, D.199 Chain B: R.157, V.164, F.166, D.199, A.203 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.157, B:R.157 Water bridges: A:R.157

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 7 residues within 4Å: Chain A: E.12, G.13, L.14, D.214, G.215, I.216 Ligands: GDP.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.12, A:G.13, A:L.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nocek, B. et al., Structure of an Amide Bond Forming F(420):gammagamma-glutamyl Ligase from Archaeoglobus Fulgidus - A Member of a New Family of Non-ribosomal Peptide Synthases. J.Mol.Biol. (2007)

Release Date

2007-05-15

Peptides

F420-0:gamma-glutamyl ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

F420-0:gamma-glutamyl ligase