SMTL ID : 6s6s.1

Structure of Azospirillum brasilense Glutamate Synthase in a4b4 oligomeric state.

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.90 Å

Oligo State

hetero-4-4-mer

Ligands

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 19 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, D.1106, G.1107, G.1108, I.1128, G.1129, T.1130 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:M.894 Hydrogen bonds: A:G.893, A:S.895, A:E.922, A:E.922, A:Q.945, A:K.1035, A:K.1035, A:S.1063, A:G.1065, A:G.1108, A:T.1130 FMN.3: 20 residues within 4Å: Chain B: M.515, P.892, G.893, M.894, S.895, Q.945, K.967, Q.970, K.1035, S.1060, S.1063, G.1064, G.1065, T.1066, D.1106, G.1107, G.1108, I.1128, G.1129, T.1130 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.893, B:S.895, B:Q.945, B:K.967, B:K.1035, B:K.1035, B:S.1060, 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, A.898, E.922, Q.945, K.967, Q.970, K.1035, G.1064, G.1065, T.1066, D.1106, G.1107, G.1108, I.1128, G.1129, T.1130, C.1154 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:A.898 Hydrogen bonds: C:G.893, C:S.895, C:E.922, C:Q.945, C:Q.945, C:K.1035, C:K.1035, C:G.1065, C:G.1065, C:G.1107, C:G.1108, C:L.1109, C:T.1130 FMN.7: 18 residues within 4Å: Chain D: P.892, G.893, M.894, S.895, E.922, Q.945, K.967, K.1035, S.1063, G.1064, G.1065, T.1066, D.1106, G.1107, G.1108, I.1128, G.1129, T.1130 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:M.894 Hydrogen bonds: D:G.893, D:S.895, D:Q.945, D:Q.945, D:K.1035, D:K.1035, D:S.1063, D:G.1065, D:G.1108, D:T.1130

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

F3S.2: 11 residues within 4Å: Chain A: M.515, C.1138, I.1139, M.1140, V.1141, R.1142, C.1144, C.1149, V.1151, 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: M.515, 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: 9 residues within 4Å: Chain C: M.515, C.1138, I.1139, M.1140, V.1141, R.1142, 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: M.515, C.1138, I.1139, M.1140, V.1141, R.1142, Q.1143, C.1144, C.1149, V.1153 3 PLIP interactions: 3 interactions with chain D, Metal complexes: D:C.1138, D:C.1144, D:C.1149

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

SF4.9: 13 residues within 4Å: Chain E: C.48, S.49, Q.50, C.51, P.54, F.55, C.56, I.66, P.67, L.70, C.109, V.110, I.111 5 PLIP interactions: 5 interactions with chain E, Metal complexes: E:C.48, E:C.51, E:C.56, E:C.56, E:C.109 SF4.10: 9 residues within 4Å: Chain E: C.60, N.64, C.95, C.99, Q.101, C.105, I.121, E.125, V.452 8 PLIP interactions: 8 interactions with chain E, Salt bridges: E:E.125, E:E.125, E:E.125 Metal complexes: E:C.60, E:C.99, E:C.105, E:E.125, E:E.125 SF4.12: 10 residues within 4Å: Chain F: C.48, S.49, Q.50, C.51, C.56, P.67, C.109, V.110, I.111, V.119 5 PLIP interactions: 5 interactions with chain F, Metal complexes: F:C.48, F:C.48, F:C.51, F:C.56, F:C.109 SF4.13: 8 residues within 4Å: Chain F: C.60, P.61, I.66, C.95, C.99, C.105, I.121, E.125 7 PLIP interactions: 7 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:E.125 SF4.15: 13 residues within 4Å: Chain G: C.48, S.49, Q.50, C.51, P.54, C.56, P.67, L.70, C.109, V.110, I.111, V.119, I.121 5 PLIP interactions: 5 interactions with chain G, Metal complexes: G:C.48, G:C.48, G:C.51, G:C.56, G:C.109 SF4.16: 12 residues within 4Å: Chain G: C.60, P.61, V.62, N.64, N.89, C.95, G.96, C.99, L.104, C.105, I.121, 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 SF4.18: 10 residues within 4Å: Chain H: C.48, S.49, C.51, F.55, C.56, I.66, P.67, C.109, V.110, I.111 5 PLIP interactions: 5 interactions with chain H, Metal complexes: H:C.48, H:S.49, H:C.51, H:C.56, H:C.109 SF4.19: 9 residues within 4Å: Chain H: C.60, N.64, I.66, C.95, C.99, C.105, I.121, G.122, E.125 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

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

FAD.11: 23 residues within 4Å: Chain E: I.98, P.100, I.154, G.155, A.156, G.157, P.158, A.159, D.178, R.179, Y.180, G.185, L.186, I.191, V.221, A.240, T.241, G.242, Y.244, D.300, D.443, S.449, L.450 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:I.98, E:I.191, E:L.450 Hydrogen bonds: E:A.156, E:A.159, E:D.178, E:R.179, E:R.179, E:Y.180, E:L.186, E:T.241, E:D.443, E:S.449 FAD.14: 26 residues within 4Å: Chain F: I.98, P.100, I.154, G.155, G.157, P.158, A.159, D.178, R.179, Y.180, G.185, L.186, G.190, I.191, K.195, V.221, A.240, T.241, G.242, Y.244, T.301, D.304, D.443, S.449, L.450, V.451 18 PLIP interactions: 18 interactions with chain F Hydrophobic interactions: F:I.98, F:I.191, F:K.195, F:L.450 Hydrogen bonds: F:A.156, F:G.157, F:A.159, F:R.179, F:R.179, F:Y.180, F:L.186, F:V.221, F:T.241, F:Y.244, F:Y.244, F:E.405, F:D.443 pi-Cation interactions: F:R.179 FAD.17: 27 residues within 4Å: Chain G: I.98, I.154, G.155, A.156, G.157, P.158, A.159, D.178, R.179, Y.180, G.185, L.186, I.191, K.195, V.221, A.240, T.241, G.242, V.243, Y.244, D.300, T.301, G.442, D.443, S.449, L.450, A.454 13 PLIP interactions: 13 interactions with chain G Hydrophobic interactions: G:I.98, G:I.191, G:L.450 Hydrogen bonds: G:A.156, G:A.159, G:R.179, G:R.179, G:L.186, G:T.241, G:V.243, G:Y.244, G:D.443, G:S.449 FAD.20: 24 residues within 4Å: Chain H: I.98, P.100, G.155, A.156, G.157, P.158, A.159, D.178, R.179, Y.180, G.185, L.186, I.191, F.219, E.220, V.221, A.240, T.241, G.242, Y.244, D.300, D.443, S.449, L.450 19 PLIP interactions: 19 interactions with chain H Hydrophobic interactions: H:I.98, H:L.450 Hydrogen bonds: H:A.156, H:G.157, H:A.159, H:R.179, H:R.179, H:Y.180, H:G.185, H:V.221, H:T.241, H:T.241, H:T.241, H:Y.244, H:D.443, H:D.443, H:D.443, H:S.449 pi-Cation interactions: H: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: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
G

F
E

G
F

H
H

Glutamate synthase [NADPH] large chain

Glutamate synthase [NADPH] small chain

Related Entries With Identical Sequence