SMTL ID : 7mft.1 (2 other biounits)

Glutamate synthase, glutamate dehydrogenase counter-enzyme complex (GudB6-GltA6-GltB6)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-6-mer

Ligands

6 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 27 residues within 4Å: Chain B: S.492, M.493, G.867, A.868, M.869, S.870, S.873, L.874, Q.920, K.942, Q.945, G.946, K.1010, S.1035, G.1039, G.1040, T.1041, G.1042, D.1081, G.1082, K.1083, L.1084, F.1103, A.1104, T.1105, A.1106, L.1108 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:A.868, B:Q.920, B:Q.920, B:K.942, B:K.1010, B:G.1040, B:G.1082, B:G.1082, B:K.1083, B:L.1084, B:A.1104, B:T.1105 Salt bridges: B:K.1083 FMN.6: 27 residues within 4Å: Chain E: S.492, M.493, G.867, A.868, M.869, S.870, S.873, L.874, Q.920, K.942, Q.945, G.946, K.1010, S.1035, G.1039, G.1040, T.1041, G.1042, D.1081, G.1082, K.1083, L.1084, F.1103, A.1104, T.1105, A.1106, L.1108 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:A.868, E:Q.920, E:Q.920, E:K.942, E:K.1010, E:G.1040, E:G.1082, E:G.1082, E:K.1083, E:L.1084, E:A.1104, E:T.1105 Salt bridges: E:K.1083 FMN.11: 27 residues within 4Å: Chain H: S.492, M.493, G.867, A.868, M.869, S.870, S.873, L.874, Q.920, K.942, Q.945, G.946, K.1010, S.1035, G.1039, G.1040, T.1041, G.1042, D.1081, G.1082, K.1083, L.1084, F.1103, A.1104, T.1105, A.1106, L.1108 13 PLIP interactions: 13 interactions with chain H Hydrogen bonds: H:A.868, H:Q.920, H:Q.920, H:K.942, H:K.1010, H:G.1040, H:G.1082, H:G.1082, H:K.1083, H:L.1084, H:A.1104, H:T.1105 Salt bridges: H:K.1083 FMN.16: 27 residues within 4Å: Chain K: S.492, M.493, G.867, A.868, M.869, S.870, S.873, L.874, Q.920, K.942, Q.945, G.946, K.1010, S.1035, G.1039, G.1040, T.1041, G.1042, D.1081, G.1082, K.1083, L.1084, F.1103, A.1104, T.1105, A.1106, L.1108 13 PLIP interactions: 13 interactions with chain K Hydrogen bonds: K:A.868, K:Q.920, K:Q.920, K:K.942, K:K.1010, K:G.1040, K:G.1082, K:G.1082, K:K.1083, K:L.1084, K:A.1104, K:T.1105 Salt bridges: K:K.1083 FMN.21: 27 residues within 4Å: Chain N: S.492, M.493, G.867, A.868, M.869, S.870, S.873, L.874, Q.920, K.942, Q.945, G.946, K.1010, S.1035, G.1039, G.1040, T.1041, G.1042, D.1081, G.1082, K.1083, L.1084, F.1103, A.1104, T.1105, A.1106, L.1108 13 PLIP interactions: 13 interactions with chain N Hydrogen bonds: N:A.868, N:Q.920, N:Q.920, N:K.942, N:K.1010, N:G.1040, N:G.1082, N:G.1082, N:K.1083, N:L.1084, N:A.1104, N:T.1105 Salt bridges: N:K.1083 FMN.26: 27 residues within 4Å: Chain Q: S.492, M.493, G.867, A.868, M.869, S.870, S.873, L.874, Q.920, K.942, Q.945, G.946, K.1010, S.1035, G.1039, G.1040, T.1041, G.1042, D.1081, G.1082, K.1083, L.1084, F.1103, A.1104, T.1105, A.1106, L.1108 13 PLIP interactions: 13 interactions with chain Q Hydrogen bonds: Q:A.868, Q:Q.920, Q:Q.920, Q:K.942, Q:K.1010, Q:G.1040, Q:G.1082, Q:G.1082, Q:K.1083, Q:L.1084, Q:A.1104, Q:T.1105 Salt bridges: Q:K.1083

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

F3S.2: 12 residues within 4Å: Chain B: M.493, C.1113, V.1114, M.1115, M.1116, R.1117, A.1118, C.1119, C.1124, P.1125, V.1128, A.1129 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.1113, B:C.1119, B:C.1124 F3S.7: 12 residues within 4Å: Chain E: M.493, C.1113, V.1114, M.1115, M.1116, R.1117, A.1118, C.1119, C.1124, P.1125, V.1128, A.1129 3 PLIP interactions: 3 interactions with chain E, Metal complexes: E:C.1113, E:C.1119, E:C.1124 F3S.12: 12 residues within 4Å: Chain H: M.493, C.1113, V.1114, M.1115, M.1116, R.1117, A.1118, C.1119, C.1124, P.1125, V.1128, A.1129 3 PLIP interactions: 3 interactions with chain H, Metal complexes: H:C.1113, H:C.1119, H:C.1124 F3S.17: 12 residues within 4Å: Chain K: M.493, C.1113, V.1114, M.1115, M.1116, R.1117, A.1118, C.1119, C.1124, P.1125, V.1128, A.1129 3 PLIP interactions: 3 interactions with chain K, Metal complexes: K:C.1113, K:C.1119, K:C.1124 F3S.22: 12 residues within 4Å: Chain N: M.493, C.1113, V.1114, M.1115, M.1116, R.1117, A.1118, C.1119, C.1124, P.1125, V.1128, A.1129 3 PLIP interactions: 3 interactions with chain N, Metal complexes: N:C.1113, N:C.1119, N:C.1124 F3S.27: 12 residues within 4Å: Chain Q: M.493, C.1113, V.1114, M.1115, M.1116, R.1117, A.1118, C.1119, C.1124, P.1125, V.1128, A.1129 3 PLIP interactions: 3 interactions with chain Q, Metal complexes: Q:C.1113, Q:C.1119, Q:C.1124

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

FAD.3: 39 residues within 4Å: Chain C: V.105, C.106, P.107, V.158, G.159, S.160, G.161, P.162, A.163, G.164, F.181, E.182, R.183, G.189, L.190, L.191, I.195, K.199, E.224, I.225, C.244, T.245, G.246, A.247, Q.248, M.267, L.270, D.302, T.303, D.306, F.421, E.425, L.429, D.460, Q.465, S.466, L.467, I.468, A.471 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:V.105, C:L.467, C:I.468 Hydrogen bonds: C:S.160, C:G.161, C:A.163, C:R.183, C:R.183, C:L.190, C:T.245, C:A.247, C:Q.248, C:D.460, C:S.466, C:S.466 pi-Cation interactions: C:R.183 FAD.8: 39 residues within 4Å: Chain F: V.105, C.106, P.107, V.158, G.159, S.160, G.161, P.162, A.163, G.164, F.181, E.182, R.183, G.189, L.190, L.191, I.195, K.199, E.224, I.225, C.244, T.245, G.246, A.247, Q.248, M.267, L.270, D.302, T.303, D.306, F.421, E.425, L.429, D.460, Q.465, S.466, L.467, I.468, A.471 16 PLIP interactions: 16 interactions with chain F Hydrophobic interactions: F:V.105, F:L.467, F:I.468 Hydrogen bonds: F:S.160, F:G.161, F:A.163, F:R.183, F:R.183, F:L.190, F:T.245, F:A.247, F:Q.248, F:D.460, F:S.466, F:S.466 pi-Cation interactions: F:R.183 FAD.13: 39 residues within 4Å: Chain I: V.105, C.106, P.107, V.158, G.159, S.160, G.161, P.162, A.163, G.164, F.181, E.182, R.183, G.189, L.190, L.191, I.195, K.199, E.224, I.225, C.244, T.245, G.246, A.247, Q.248, M.267, L.270, D.302, T.303, D.306, F.421, E.425, L.429, D.460, Q.465, S.466, L.467, I.468, A.471 16 PLIP interactions: 16 interactions with chain I Hydrophobic interactions: I:V.105, I:L.467, I:I.468 Hydrogen bonds: I:S.160, I:G.161, I:A.163, I:R.183, I:R.183, I:L.190, I:T.245, I:A.247, I:Q.248, I:D.460, I:S.466, I:S.466 pi-Cation interactions: I:R.183 FAD.18: 39 residues within 4Å: Chain L: V.105, C.106, P.107, V.158, G.159, S.160, G.161, P.162, A.163, G.164, F.181, E.182, R.183, G.189, L.190, L.191, I.195, K.199, E.224, I.225, C.244, T.245, G.246, A.247, Q.248, M.267, L.270, D.302, T.303, D.306, F.421, E.425, L.429, D.460, Q.465, S.466, L.467, I.468, A.471 18 PLIP interactions: 18 interactions with chain L Hydrophobic interactions: L:V.105, L:L.467, L:I.468 Hydrogen bonds: L:S.160, L:G.161, L:A.163, L:R.183, L:R.183, L:L.190, L:T.245, L:A.247, L:Q.248, L:D.302, L:D.306, L:D.460, L:S.466, L:S.466 pi-Cation interactions: L:R.183 FAD.23: 39 residues within 4Å: Chain O: V.105, C.106, P.107, V.158, G.159, S.160, G.161, P.162, A.163, G.164, F.181, E.182, R.183, G.189, L.190, L.191, I.195, K.199, E.224, I.225, C.244, T.245, G.246, A.247, Q.248, M.267, L.270, D.302, T.303, D.306, F.421, E.425, L.429, D.460, Q.465, S.466, L.467, I.468, A.471 18 PLIP interactions: 18 interactions with chain O Hydrophobic interactions: O:V.105, O:L.467, O:I.468 Hydrogen bonds: O:S.160, O:G.161, O:A.163, O:R.183, O:R.183, O:L.190, O:T.245, O:A.247, O:Q.248, O:D.302, O:D.306, O:D.460, O:S.466, O:S.466 pi-Cation interactions: O:R.183 FAD.28: 39 residues within 4Å: Chain R: V.105, C.106, P.107, V.158, G.159, S.160, G.161, P.162, A.163, G.164, F.181, E.182, R.183, G.189, L.190, L.191, I.195, K.199, E.224, I.225, C.244, T.245, G.246, A.247, Q.248, M.267, L.270, D.302, T.303, D.306, F.421, E.425, L.429, D.460, Q.465, S.466, L.467, I.468, A.471 18 PLIP interactions: 18 interactions with chain R Hydrophobic interactions: R:V.105, R:L.467, R:I.468 Hydrogen bonds: R:S.160, R:G.161, R:A.163, R:R.183, R:R.183, R:L.190, R:T.245, R:A.247, R:Q.248, R:D.302, R:D.306, R:D.460, R:S.466, R:S.466 pi-Cation interactions: R:R.183

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

SF4.4: 12 residues within 4Å: Chain C: C.46, M.47, C.49, P.52, F.53, C.54, P.74, C.114, T.115, L.116, V.123, I.125 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.46, C:C.49, C:C.54, C:C.114 SF4.5: 14 residues within 4Å: Chain C: C.67, I.69, N.71, I.73, W.76, T.102, C.106, A.108, P.109, C.110, I.125, K.126, E.129, V.469 7 PLIP interactions: 7 interactions with chain C, Salt bridges: C:E.129, C:E.129, C:E.129 Metal complexes: C:C.67, C:C.106, C:C.110, C:E.129 SF4.9: 12 residues within 4Å: Chain F: C.46, M.47, C.49, P.52, F.53, C.54, P.74, C.114, T.115, L.116, V.123, I.125 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.46, F:C.49, F:C.54, F:C.114 SF4.10: 14 residues within 4Å: Chain F: C.67, I.69, N.71, I.73, W.76, T.102, C.106, A.108, P.109, C.110, I.125, K.126, E.129, V.469 7 PLIP interactions: 7 interactions with chain F, Salt bridges: F:E.129, F:E.129, F:E.129 Metal complexes: F:C.67, F:C.106, F:C.110, F:E.129 SF4.14: 12 residues within 4Å: Chain I: C.46, M.47, C.49, P.52, F.53, C.54, P.74, C.114, T.115, L.116, V.123, I.125 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.46, I:C.49, I:C.54, I:C.114 SF4.15: 14 residues within 4Å: Chain I: C.67, I.69, N.71, I.73, W.76, T.102, C.106, A.108, P.109, C.110, I.125, K.126, E.129, V.469 7 PLIP interactions: 7 interactions with chain I, Salt bridges: I:E.129, I:E.129, I:E.129 Metal complexes: I:C.67, I:C.106, I:C.110, I:E.129 SF4.19: 12 residues within 4Å: Chain L: C.46, M.47, C.49, P.52, F.53, C.54, P.74, C.114, T.115, L.116, V.123, I.125 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:C.46, L:C.49, L:C.54, L:C.114 SF4.20: 14 residues within 4Å: Chain L: C.67, I.69, N.71, I.73, W.76, T.102, C.106, A.108, P.109, C.110, I.125, K.126, E.129, V.469 7 PLIP interactions: 7 interactions with chain L, Salt bridges: L:E.129, L:E.129, L:E.129 Metal complexes: L:C.67, L:C.106, L:C.110, L:E.129 SF4.24: 12 residues within 4Å: Chain O: C.46, M.47, C.49, P.52, F.53, C.54, P.74, C.114, T.115, L.116, V.123, I.125 4 PLIP interactions: 4 interactions with chain O, Metal complexes: O:C.46, O:C.49, O:C.54, O:C.114 SF4.25: 14 residues within 4Å: Chain O: C.67, I.69, N.71, I.73, W.76, T.102, C.106, A.108, P.109, C.110, I.125, K.126, E.129, V.469 7 PLIP interactions: 7 interactions with chain O, Salt bridges: O:E.129, O:E.129, O:E.129 Metal complexes: O:C.67, O:C.106, O:C.110, O:E.129 SF4.29: 12 residues within 4Å: Chain R: C.46, M.47, C.49, P.52, F.53, C.54, P.74, C.114, T.115, L.116, V.123, I.125 4 PLIP interactions: 4 interactions with chain R, Metal complexes: R:C.46, R:C.49, R:C.54, R:C.114 SF4.30: 14 residues within 4Å: Chain R: C.67, I.69, N.71, I.73, W.76, T.102, C.106, A.108, P.109, C.110, I.125, K.126, E.129, V.469 7 PLIP interactions: 7 interactions with chain R, Salt bridges: R:E.129, R:E.129, R:E.129 Metal complexes: R:C.67, R:C.106, R:C.110, R:E.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jayaraman, V. et al., A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis. Nat.Chem.Biol. (2022)

Release Date

2022-01-05

Peptides

Glutamate dehydrogenase: ADGJMP
Glutamate synthase (NADPH) large chain: BEHKNQ
Glutamate synthase (NADPH) small chain: CFILOR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

J
A

M
A

P
A

B
G

E
G

H
G

K
G

N
G

Q
G

C
I

F
I

I
I

L
I

O
I

R
I

Glutamate dehydrogenase

Glutamate synthase (NADPH) large chain

Glutamate synthase (NADPH) small chain

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