SMTL ID : 7zc6.1

Na+ - translocating ferredoxin: NAD+ reductase (Rnf) of C. tetanomorphum

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-mer

Ligands

1 x FE: FE (III) ION(Non-covalent)

FE.1: 4 residues within 4Å: Chain A: C.25, C.113 Chain E: C.26, C.109 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain E Metal complexes: A:C.25, A:C.113, E:C.26, E:C.109

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

SF4.2: 8 residues within 4Å: Chain B: C.152, F.154, C.171, T.172, G.173, C.174, G.175, C.177 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.152, B:C.171, B:C.174, B:C.177 SF4.3: 7 residues within 4Å: Chain B: C.124, C.142, G.146, S.147, C.148, A.164, C.181 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.124, B:C.142, B:C.148, B:C.181 SF4.4: 10 residues within 4Å: Chain B: K.104, C.105, Q.106, G.107, C.138, G.141, C.199, N.200, C.212, V.214 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.105, B:C.138, B:C.199, B:C.212 SF4.5: 9 residues within 4Å: Chain B: C.216, L.217, S.218, C.219, G.220, L.221, C.222, M.233, C.255 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.216, B:C.219, B:C.222, B:C.255 SF4.6: 11 residues within 4Å: Chain B: V.195, C.226, S.228, I.240, C.245, T.246, Q.247, C.248, G.249, V.250, C.251 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.226, B:C.245, B:C.248, B:C.251 SF4.7: 10 residues within 4Å: Chain C: C.375, P.376, P.381, C.404, I.405, E.406, C.407, G.408, C.410, L.421 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.375, C:C.404, C:C.407, C:C.410 SF4.8: 8 residues within 4Å: Chain C: C.365, I.366, C.368, G.369, C.371, T.382, C.414, L.420 5 PLIP interactions: 5 interactions with chain C, Metal complexes: C:C.365, C:C.368, C:C.371, C:T.382, C:C.414

3 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)(Covalent)

FMN.9: 18 residues within 4Å: Chain C: G.134, M.135, G.136, G.137, A.138, K.145, N.160, A.162, E.163, C.164, G.235, A.236, Q.263, N.264, T.267, M.331, I.405, C.407 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:A.236 Hydrogen bonds: C:A.138, C:N.160, C:E.163, C:C.164, C:G.235, C:E.237, C:Q.263, C:N.264, C:T.267 Salt bridges: C:K.145 FMN.10: 16 residues within 4Å: Chain D: N.90, L.127, R.130, W.144, T.153, A.156, C.182, E.185, G.237, L.240, P.280, E.281, V.283, S.284, Y.285 Ligands: FMN.12 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:L.127, D:L.240, D:V.283, D:V.283 Hydrogen bonds: D:R.130, D:R.130, D:T.153, D:A.156, D:E.185, D:G.237, D:E.281, D:S.284 pi-Cation interactions: D:R.130, D:R.130 FMN.12: 11 residues within 4Å: Chain D: L.134, E.162, Y.279 Chain F: Y.93, L.123, G.162, A.163, T.164, I.165, T.166 Ligands: FMN.10 7 PLIP interactions: 3 interactions with chain F, 4 interactions with chain D Hydrogen bonds: F:G.162, F:T.164, F:T.166, D:E.162 Hydrophobic interactions: D:L.134, D:L.134, D:Y.279

1 x RBF: RIBOFLAVIN(Non-covalent)

RBF.11: 14 residues within 4Å: Chain D: I.24, M.25, V.28, S.79, V.82, L.86, K.112, N.121, P.125, F.244, M.245, D.248, Y.249, A.250 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.24, D:V.28, D:Y.249 Hydrogen bonds: D:N.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vitt, S. et al., Purification and structural characterization of the Na + -translocating ferredoxin: NAD + reductase (Rnf) complex of Clostridium tetanomorphum. Nat Commun (2022)

Release Date

2022-09-28

Peptides

RnfA: A
RnfB: B
RnfC: C
RnfD: D
RnfE: E
RnfG: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
G

Membrane

We predict this structure to be a membrane protein.
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RnfA

RnfB

RnfC

RnfD

RnfE

RnfG