SMTL ID : 6s6t.1

Structure of Azospirillum brasilense Glutamate Synthase in a4b3 oligomeric state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.10 Å

Oligo State

hetero-4-3-mer

Ligands

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 22 residues within 4Å: Chain A: M.515, P.892, G.893, M.894, S.895, E.922, Q.945, K.967, Q.970, K.1035, S.1063, G.1064, G.1065, T.1066, G.1067, D.1106, G.1107, G.1108, G.1127, I.1128, G.1129, T.1130 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.893, A:S.895, A:E.922, A:Q.945, A:Q.970, A:K.1035, A:K.1035, A:G.1065, A:G.1065, A:G.1107, A:G.1108, A:L.1109, A:G.1127, A:T.1130 FMN.3: 19 residues within 4Å: Chain B: P.892, G.893, M.894, S.895, E.922, Q.945, K.967, Q.970, K.1035, S.1063, G.1064, G.1065, T.1066, D.1106, G.1107, G.1108, I.1128, G.1129, T.1130 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:G.893, B:S.895, B:E.922, B:Q.945, B:Q.945, B:Q.970, B:K.1035, B:K.1035, B:G.1065, B:D.1106, B:D.1106, B:G.1107, B:G.1108, B:T.1130 FMN.5: 21 residues within 4Å: Chain C: M.515, P.892, G.893, M.894, S.895, L.899, E.922, Q.945, K.967, Q.970, K.1035, S.1063, G.1064, G.1065, T.1066, G.1107, G.1108, I.1128, G.1129, T.1130, C.1154 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:G.893, C:S.895, C:Q.945, C:Q.945, C:Q.970, C:K.1035, C:K.1035, C:G.1065, C:G.1107, C:G.1108, C:G.1127, C:T.1130, C:A.1131 FMN.7: 18 residues within 4Å: Chain D: P.892, G.893, S.895, L.899, E.922, K.967, Q.970, K.1035, S.1063, G.1064, G.1065, T.1066, D.1106, G.1107, G.1108, I.1128, G.1129, T.1130 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:L.899, D:T.1130 Hydrogen bonds: D:G.893, D:S.895, D:E.922, D:E.922, D:Q.970, D:K.1035, D:K.1035, D:G.1065, D:G.1107, D:G.1108, D:I.1128, D:T.1130, D:T.1130, D:A.1131

4 x F3S: FE3-S4 CLUSTER(Covalent)(Non-covalent)

F3S.2: 10 residues within 4Å: Chain A: M.515, C.1138, I.1139, M.1140, V.1141, R.1142, C.1144, C.1149, V.1153, C.1154 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.1138, A:C.1144, A:C.1149 F3S.4: 11 residues within 4Å: Chain B: C.1138, I.1139, M.1140, V.1141, R.1142, Q.1143, C.1144, C.1149, P.1150, V.1153, C.1154 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.1138, B:C.1144, B:C.1149, B:C.1149 F3S.6: 11 residues within 4Å: Chain C: M.515, C.1138, M.1140, V.1141, R.1142, Q.1143, C.1144, C.1149, P.1150, V.1151, C.1154 3 PLIP interactions: 3 interactions with chain C, Metal complexes: C:C.1138, C:C.1144, C:C.1149 F3S.8: 10 residues within 4Å: Chain D: M.515, C.1138, I.1139, M.1140, V.1141, R.1142, C.1144, C.1149, V.1151, C.1154 3 PLIP interactions: 3 interactions with chain D, Metal complexes: D:C.1138, D:C.1144, D:C.1149

6 x SF4: IRON/SULFUR CLUSTER(Covalent)(Non-covalent)

SF4.9: 8 residues within 4Å: Chain E: C.48, S.49, C.51, P.54, C.56, I.66, C.109, V.110 5 PLIP interactions: 5 interactions with chain E, Metal complexes: E:C.48, E:C.51, E:C.51, E:C.56, E:C.109 SF4.10: 7 residues within 4Å: Chain E: C.60, V.62, N.64, C.95, C.99, C.105, E.125 9 PLIP interactions: 9 interactions with chain E, Salt bridges: E:E.125, E:E.125, E:E.125 Metal complexes: E:C.60, E:C.60, E:C.99, E:C.105, E:C.105, E:E.125 SF4.12: 9 residues within 4Å: Chain F: C.48, S.49, C.51, P.54, C.56, C.109, V.110, I.111, V.119 6 PLIP interactions: 6 interactions with chain F, Metal complexes: F:C.48, F:C.48, F:C.51, F:C.56, F:C.109, F:C.109 SF4.13: 8 residues within 4Å: Chain F: C.60, V.62, C.95, C.99, C.105, G.122, E.125, V.452 8 PLIP interactions: 8 interactions with chain F, Salt bridges: F:E.125, F:E.125, F:E.125 Metal complexes: F:C.60, F:C.99, F:C.105, F:C.105, F:E.125 SF4.15: 9 residues within 4Å: Chain G: C.48, S.49, C.51, P.54, F.55, C.56, P.67, C.109, V.110 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.48, G:C.51, G:C.56, G:C.109 SF4.16: 11 residues within 4Å: Chain G: C.60, P.61, N.64, C.95, C.99, L.104, C.105, I.121, G.122, E.125, V.452 9 PLIP interactions: 9 interactions with chain G, Salt bridges: G:E.125, G:E.125, G:E.125 Metal complexes: G:C.60, G:C.99, G:C.105, G:C.105, G:E.125, G:E.125

3 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.11: 24 residues within 4Å: Chain E: I.98, P.100, G.155, A.156, G.157, P.158, A.159, Y.177, D.178, R.179, G.185, L.186, F.219, V.221, A.240, T.241, G.242, Y.244, D.300, D.304, F.402, D.443, S.449, V.451 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:I.98, E:V.451 Hydrogen bonds: E:A.156, E:A.159, E:R.179, E:Y.180, E:G.185, E:L.186, E:V.221, E:S.449 pi-Cation interactions: E:R.179 FAD.14: 25 residues within 4Å: Chain F: I.98, G.155, A.156, G.157, P.158, A.159, G.160, D.178, R.179, G.185, L.186, I.191, F.219, E.220, V.221, A.240, T.241, G.242, Y.244, T.301, D.304, D.443, S.449, L.450, V.451 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:I.98, F:I.191 Hydrogen bonds: F:A.156, F:A.159, F:G.160, F:R.179, F:L.186, F:V.221, F:Y.244, F:D.443, F:S.449 FAD.17: 27 residues within 4Å: Chain G: I.98, G.155, A.156, G.157, P.158, Y.177, D.178, R.179, Y.180, G.185, L.186, G.190, I.191, K.195, F.219, E.220, V.221, A.240, T.241, G.242, Y.244, D.304, D.443, S.449, L.450, V.451, A.454 15 PLIP interactions: 15 interactions with chain G Hydrophobic interactions: G:I.98, G:I.98, G:I.191, G:L.450 Hydrogen bonds: G:A.156, G:G.157, G:R.179, G:Y.180, G:G.185, G:L.186, G:V.221, G:T.241, G:Y.244, G:Y.244 pi-Cation interactions: G:R.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Swuec, P. et al., Cryo-EM Structures of Azospirillum brasilense Glutamate Synthase in Its Oligomeric Assemblies. J.Mol.Biol. (2019)

Release Date

2019-09-11

Peptides

Glutamate synthase [NADPH] large chain: ABCD
Glutamate synthase [NADPH] small chain: EFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Glutamate synthase [NADPH] large chain

Glutamate synthase [NADPH] small chain

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