SMTL ID : 6s6x.1

Structure of Azospirillum brasilense Glutamate Synthase in a6b6 oligomeric state.

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-mer

Ligands

6 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 20 residues within 4Å: Chain A: 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, I.1128, G.1129, T.1130 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.893, A:G.893, A:S.895, A:E.922, A:Q.945, A:Q.945, A:K.1035, A:K.1035, A:K.1035, A:G.1065, A:G.1107, A:G.1108, A:T.1130, A:T.1130 FMN.3: 20 residues within 4Å: Chain B: 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, D.1106, G.1107, G.1108, I.1128, G.1129, T.1130 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:M.894, B:L.899 Hydrogen bonds: B:G.893, B:G.893, B:S.895, B:E.922, B:Q.945, B:Q.945, B:K.1035, B:K.1035, B:K.1035, B:G.1065, B:G.1107, B:G.1108, B:T.1130 FMN.5: 20 residues within 4Å: Chain C: 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, D.1106, G.1107, G.1108, I.1128, G.1129, T.1130 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:L.899 Hydrogen bonds: C:G.893, C:G.893, C:S.895, C:E.922, C:Q.945, C:Q.945, C:K.1035, C:K.1035, C:K.1035, C:G.1065, C:G.1107, C:G.1108, C:T.1130, C:T.1130 FMN.7: 20 residues within 4Å: Chain D: 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, I.1128, G.1129, T.1130 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:G.893, D:G.893, D:S.895, D:E.922, D:Q.945, D:Q.945, D:K.1035, D:K.1035, D:K.1035, D:G.1065, D:G.1107, D:G.1108, D:T.1130, D:T.1130 FMN.9: 20 residues within 4Å: Chain E: 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, D.1106, G.1107, G.1108, I.1128, G.1129, T.1130 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:M.894, E:L.899 Hydrogen bonds: E:G.893, E:G.893, E:S.895, E:E.922, E:Q.945, E:Q.945, E:K.1035, E:K.1035, E:K.1035, E:G.1065, E:G.1107, E:G.1108, E:T.1130 FMN.11: 20 residues within 4Å: Chain F: 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, D.1106, G.1107, G.1108, I.1128, G.1129, T.1130 16 PLIP interactions: 16 interactions with chain F Hydrophobic interactions: F:L.899 Hydrogen bonds: F:G.893, F:G.893, F:S.895, F:E.922, F:Q.945, F:Q.945, F:K.1035, F:K.1035, F:K.1035, F:G.1065, F:G.1107, F:G.1108, F:T.1130, F:T.1130, F:T.1130

6 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.2: 10 residues within 4Å: Chain A: C.1138, I.1139, M.1140, V.1141, R.1142, Q.1143, 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: 10 residues within 4Å: Chain B: C.1138, I.1139, M.1140, V.1141, R.1142, Q.1143, C.1144, C.1149, V.1153, C.1154 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.1138, B:C.1144, B:C.1149 F3S.6: 10 residues within 4Å: Chain C: M.515, C.1138, I.1139, M.1140, V.1141, R.1142, Q.1143, C.1144, C.1149, 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: C.1138, I.1139, M.1140, V.1141, R.1142, Q.1143, C.1144, C.1149, V.1153, C.1154 3 PLIP interactions: 3 interactions with chain D, Metal complexes: D:C.1138, D:C.1144, D:C.1149 F3S.10: 10 residues within 4Å: Chain E: C.1138, I.1139, M.1140, V.1141, R.1142, Q.1143, C.1144, C.1149, V.1153, C.1154 3 PLIP interactions: 3 interactions with chain E, Metal complexes: E:C.1138, E:C.1144, E:C.1149 F3S.12: 10 residues within 4Å: Chain F: M.515, C.1138, I.1139, M.1140, V.1141, R.1142, Q.1143, C.1144, C.1149, C.1154 3 PLIP interactions: 3 interactions with chain F, Metal complexes: F:C.1138, F:C.1144, F:C.1149

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

SF4.13: 8 residues within 4Å: Chain G: C.48, S.49, C.51, C.56, P.67, C.109, V.110, V.119 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.48, G:C.51, G:C.56, G:C.109 SF4.14: 9 residues within 4Å: Chain G: C.60, N.64, I.66, C.95, C.99, Q.101, L.104, C.105, E.125 7 PLIP interactions: 7 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:E.125 SF4.16: 9 residues within 4Å: Chain H: C.48, S.49, C.51, F.55, C.56, P.67, C.109, V.110, I.111 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.48, H:C.51, H:C.56, H:C.109 SF4.17: 12 residues within 4Å: Chain H: C.60, N.64, I.66, C.95, C.99, Q.101, L.104, C.105, I.121, G.122, E.125, V.452 7 PLIP interactions: 7 interactions with chain H, Salt bridges: H:E.125, H:E.125, H:E.125 Metal complexes: H:C.60, H:C.99, H:C.105, H:E.125 SF4.19: 8 residues within 4Å: Chain I: C.48, S.49, C.51, F.55, C.56, P.67, C.109, V.110 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.48, I:C.51, I:C.56, I:C.109 SF4.20: 13 residues within 4Å: Chain I: C.60, V.62, N.64, I.66, C.95, C.99, Q.101, L.104, C.105, I.121, G.122, E.125, V.452 7 PLIP interactions: 7 interactions with chain I, Salt bridges: I:E.125, I:E.125, I:E.125 Metal complexes: I:C.60, I:C.99, I:C.105, I:E.125 SF4.22: 8 residues within 4Å: Chain J: C.48, S.49, C.51, C.56, P.67, C.109, V.110, V.119 4 PLIP interactions: 4 interactions with chain J, Metal complexes: J:C.48, J:C.51, J:C.56, J:C.109 SF4.23: 9 residues within 4Å: Chain J: C.60, N.64, I.66, C.95, C.99, Q.101, L.104, C.105, E.125 7 PLIP interactions: 7 interactions with chain J, Salt bridges: J:E.125, J:E.125, J:E.125 Metal complexes: J:C.60, J:C.99, J:C.105, J:E.125 SF4.25: 9 residues within 4Å: Chain K: C.48, S.49, C.51, F.55, C.56, P.67, C.109, V.110, I.111 4 PLIP interactions: 4 interactions with chain K, Metal complexes: K:C.48, K:C.51, K:C.56, K:C.109 SF4.26: 12 residues within 4Å: Chain K: C.60, N.64, I.66, C.95, C.99, Q.101, L.104, C.105, I.121, G.122, E.125, V.452 7 PLIP interactions: 7 interactions with chain K, Salt bridges: K:E.125, K:E.125, K:E.125 Metal complexes: K:C.60, K:C.99, K:C.105, K:E.125 SF4.28: 8 residues within 4Å: Chain L: C.48, S.49, C.51, F.55, C.56, P.67, C.109, V.110 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:C.48, L:C.51, L:C.56, L:C.109 SF4.29: 13 residues within 4Å: Chain L: C.60, V.62, N.64, I.66, C.95, C.99, Q.101, L.104, C.105, I.121, G.122, E.125, V.452 7 PLIP interactions: 7 interactions with chain L, Salt bridges: L:E.125, L:E.125, L:E.125 Metal complexes: L:C.60, L:C.99, L:C.105, L:E.125

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

FAD.15: 27 residues within 4Å: Chain G: I.98, I.154, G.155, A.156, G.157, P.158, A.159, Y.177, D.178, R.179, Y.180, G.185, L.186, E.220, V.221, T.241, G.242, Y.244, D.300, T.301, D.304, F.402, D.443, S.449, L.450, V.451, A.454 11 PLIP interactions: 11 interactions with chain G Hydrophobic interactions: G:I.98, G:L.450 Hydrogen bonds: G:A.156, G:A.159, G:R.179, G:Y.180, G:G.185, G:L.186, G:V.221, G:T.241, G:D.443 FAD.18: 24 residues within 4Å: Chain H: I.98, G.155, A.156, G.157, P.158, Y.177, D.178, R.179, Y.180, G.185, L.186, K.195, F.219, E.220, V.221, T.241, Y.244, D.300, T.301, D.304, F.402, D.443, S.449, V.451 15 PLIP interactions: 15 interactions with chain H Hydrophobic interactions: H:I.98, H:I.98 Hydrogen bonds: H:A.156, H:R.179, H:R.179, H:G.185, H:L.186, H:V.221, H:T.241, H:T.241, H:Y.244, H:D.304, H:D.443, H:D.443, H:S.449 FAD.21: 29 residues within 4Å: Chain I: I.98, I.154, G.155, A.156, G.157, P.158, A.159, Y.177, D.178, R.179, Y.180, G.185, L.186, G.190, K.195, E.220, V.221, T.241, G.242, Y.244, D.300, T.301, D.304, F.402, D.443, S.449, L.450, V.451, A.454 13 PLIP interactions: 13 interactions with chain I Hydrophobic interactions: I:I.98 Hydrogen bonds: I:A.156, I:A.159, I:R.179, I:R.179, I:G.185, I:L.186, I:V.221, I:T.241, I:Y.244, I:D.443, I:D.443, I:S.449 FAD.24: 27 residues within 4Å: Chain J: I.98, I.154, G.155, A.156, G.157, P.158, A.159, Y.177, D.178, R.179, Y.180, G.185, L.186, E.220, V.221, A.240, T.241, G.242, Y.244, D.300, T.301, D.304, F.402, D.443, S.449, L.450, V.451 14 PLIP interactions: 14 interactions with chain J Hydrophobic interactions: J:I.98, J:L.450 Hydrogen bonds: J:A.156, J:A.159, J:R.179, J:R.179, J:G.185, J:L.186, J:V.221, J:T.241, J:D.443, J:D.443, J:D.443, J:S.449 FAD.27: 29 residues within 4Å: Chain K: I.98, P.100, I.154, G.155, G.157, P.158, A.159, Y.177, D.178, R.179, Y.180, G.185, L.186, G.190, K.195, E.220, V.221, T.241, G.242, Y.244, D.300, T.301, D.304, F.402, D.443, S.449, L.450, V.451, A.454 11 PLIP interactions: 11 interactions with chain K Hydrophobic interactions: K:I.98 Hydrogen bonds: K:A.159, K:R.179, K:L.186, K:V.221, K:T.241, K:T.241, K:Y.244, K:D.443, K:D.443, K:S.449 FAD.30: 25 residues within 4Å: Chain L: I.98, G.155, A.156, G.157, P.158, Y.177, D.178, R.179, Y.180, G.185, L.186, K.195, F.219, E.220, V.221, T.241, Y.244, D.300, T.301, D.304, F.402, D.443, S.449, L.450, V.451 18 PLIP interactions: 18 interactions with chain L Hydrophobic interactions: L:I.98, L:I.98, L:V.451 Hydrogen bonds: L:A.156, L:D.178, L:R.179, L:Y.180, L:G.185, L:L.186, L:V.221, L:T.241, L:T.241, L:Y.244, L:D.304, L:D.443, L:D.443, L:S.449 pi-Cation interactions: L: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: ABCDEF
Glutamate synthase [NADPH] small chain: GHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

Glutamate synthase [NADPH] large chain

Glutamate synthase [NADPH] small chain

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