SMTL ID : 6tga.1

Cryo-EM Structure of as isolated form of NAD+-dependent Formate Dehydrogenase from Rhodobacter capsulatus

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.26 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

4 x MGD: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE(Non-covalent)

MGD.1: 32 residues within 4Å: Chain A: R.357, C.358, C.382, V.385, C.386, L.551, E.555, Q.589, G.655, E.656, D.657, S.661, H.681, D.682, N.686, S.699, K.704, D.730, T.827, R.829, Y.834, N.835, V.836, A.838, Q.839, F.900, N.908, Y.924, K.925 Ligands: MGD.2, 6MO.3, H2S.9 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:E.555, A:Q.589, A:D.657, A:S.661, A:S.661, A:H.681, A:H.681, A:N.686, A:K.704, A:R.829, A:R.829, A:N.835, A:V.836, A:N.908, A:N.908 Salt bridges: A:R.357, A:D.730 pi-Stacking: A:F.900, A:Y.924 pi-Cation interactions: A:H.681, A:F.900 MGD.2: 37 residues within 4Å: Chain A: C.261, K.295, C.386, I.419, G.420, A.421, N.422, D.425, G.426, H.427, V.447, D.448, P.449, R.450, P.470, G.471, N.473, G.550, L.551, G.552, H.556, L.586, G.588, Q.589, T.826, G.828, R.829, I.830, L.831, Q.833, Y.834, N.835, H.901, K.925 Ligands: MGD.1, 6MO.3, H2S.9 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:K.295, A:K.295, A:G.420, A:N.422, A:G.426, A:R.450, A:G.471, A:N.473, A:N.473, A:L.551, A:N.835, A:N.835 Salt bridges: A:H.427, A:D.448, A:R.829, A:K.925 MGD.13: 32 residues within 4Å: Chain E: R.357, C.358, C.382, V.385, C.386, L.551, E.555, Q.589, G.655, E.656, D.657, S.661, H.681, D.682, N.686, S.699, K.704, D.730, T.827, R.829, Y.834, N.835, V.836, A.838, Q.839, F.900, N.908, Y.924, K.925 Ligands: MGD.14, 6MO.15, H2S.21 21 PLIP interactions: 21 interactions with chain E Hydrogen bonds: E:E.555, E:Q.589, E:D.657, E:S.661, E:S.661, E:H.681, E:H.681, E:N.686, E:K.704, E:R.829, E:R.829, E:N.835, E:V.836, E:N.908, E:N.908 Salt bridges: E:R.357, E:D.730 pi-Stacking: E:F.900, E:Y.924 pi-Cation interactions: E:H.681, E:F.900 MGD.14: 37 residues within 4Å: Chain E: C.261, K.295, C.386, I.419, G.420, A.421, N.422, D.425, G.426, H.427, V.447, D.448, P.449, R.450, P.470, G.471, N.473, G.550, L.551, G.552, H.556, L.586, G.588, Q.589, T.826, G.828, R.829, I.830, L.831, Q.833, Y.834, N.835, H.901, K.925 Ligands: MGD.13, 6MO.15, H2S.21 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:K.295, E:K.295, E:G.420, E:N.422, E:G.426, E:R.450, E:G.471, E:N.473, E:N.473, E:L.551, E:N.835, E:N.835 Salt bridges: E:H.427, E:D.448, E:R.829, E:K.925

2 x 6MO: MOLYBDENUM(VI) ION(Non-covalent)

6MO.3: 4 residues within 4Å: Chain A: C.386 Ligands: MGD.1, MGD.2, H2S.9 No protein-ligand interaction detected (PLIP) 6MO.15: 4 residues within 4Å: Chain E: C.386 Ligands: MGD.13, MGD.14, H2S.21 No protein-ligand interaction detected (PLIP)

4 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.4: 6 residues within 4Å: Chain A: C.57, V.65, G.66, C.68, C.71, C.85 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.57, A:C.68, A:C.71, A:C.85 FES.12: 9 residues within 4Å: Chain B: S.180 Chain C: C.77, A.79, C.82, C.116, L.117, G.118, L.119, C.120 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.77, C:C.82, C:C.116, C:C.120 FES.16: 6 residues within 4Å: Chain E: C.57, V.65, G.66, C.68, C.71, C.85 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.57, E:C.68, E:C.71, E:C.85 FES.24: 9 residues within 4Å: Chain F: S.180 Chain G: C.77, A.79, C.82, C.116, L.117, G.118, L.119, C.120 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.77, G:C.82, G:C.116, G:C.120

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

SF4.5: 10 residues within 4Å: Chain A: H.117, P.118, D.120, C.121, C.124, A.126, C.130, K.181, T.236, A.237 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.117, A:C.121, A:C.124, A:C.130 SF4.6: 12 residues within 4Å: Chain A: C.182, I.183, V.184, C.185, M.186, R.187, C.188, I.212, C.234, P.235, T.236, T.238 5 PLIP interactions: 5 interactions with chain A, Metal complexes: A:C.182, A:I.183, A:C.185, A:C.188, A:C.234 SF4.7: 11 residues within 4Å: Chain A: C.192, Q.196, T.198, L.201, C.224, V.225, S.226, C.227, G.228, A.229, C.230 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.192, A:C.224, A:C.227, A:C.230 SF4.8: 12 residues within 4Å: Chain A: C.258, Y.260, C.261, V.263, G.264, C.265, F.267, C.293, K.295, G.296, P.428, V.429 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.258, A:C.261, A:C.265, A:C.293 SF4.11: 13 residues within 4Å: Chain B: V.255, V.273, S.426, C.427, G.428, T.429, C.430, C.433, S.469, L.470, C.471, L.473, G.474 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.427, B:C.430, B:C.433, B:C.471 SF4.17: 10 residues within 4Å: Chain E: H.117, P.118, D.120, C.121, C.124, A.126, C.130, K.181, T.236, A.237 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:H.117, E:C.121, E:C.124, E:C.130 SF4.18: 12 residues within 4Å: Chain E: C.182, I.183, V.184, C.185, M.186, R.187, C.188, I.212, C.234, P.235, T.236, T.238 5 PLIP interactions: 5 interactions with chain E, Metal complexes: E:C.182, E:I.183, E:C.185, E:C.188, E:C.234 SF4.19: 11 residues within 4Å: Chain E: C.192, Q.196, T.198, L.201, C.224, V.225, S.226, C.227, G.228, A.229, C.230 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.192, E:C.224, E:C.227, E:C.230 SF4.20: 12 residues within 4Å: Chain E: C.258, Y.260, C.261, V.263, G.264, C.265, F.267, C.293, K.295, G.296, P.428, V.429 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.258, E:C.261, E:C.265, E:C.293 SF4.23: 13 residues within 4Å: Chain F: V.255, V.273, S.426, C.427, G.428, T.429, C.430, C.433, S.469, L.470, C.471, L.473, G.474 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.427, F:C.430, F:C.433, F:C.471

2 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.9: 6 residues within 4Å: Chain A: C.386, Q.589, V.592 Ligands: MGD.1, MGD.2, 6MO.3 No protein-ligand interaction detected (PLIP) H2S.21: 6 residues within 4Å: Chain E: C.386, Q.589, V.592 Ligands: MGD.13, MGD.14, 6MO.15 No protein-ligand interaction detected (PLIP)

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.10: 16 residues within 4Å: Chain B: G.146, R.147, G.148, K.157, N.174, D.176, E.177, G.178, Y.254, G.257, E.258, E.259, V.292, N.293, N.294, S.297 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:R.147, B:G.148, B:N.174, B:D.176, B:G.178, B:E.258, B:E.259, B:N.293, B:N.294, B:N.294, B:S.297, B:S.297 Salt bridges: B:K.157 FMN.22: 16 residues within 4Å: Chain F: G.146, R.147, G.148, K.157, N.174, D.176, E.177, G.178, Y.254, G.257, E.258, E.259, V.292, N.293, N.294, S.297 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:R.147, F:G.148, F:N.174, F:D.176, F:G.178, F:E.258, F:E.259, F:N.293, F:N.294, F:N.294, F:S.297, F:S.297 Salt bridges: F:K.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Radon, C. et al., Cryo-EM structures reveal intricate Fe-S cluster arrangement and charging in Rhodobacter capsulatus formate dehydrogenase. Nat Commun (2020)

Release Date

2020-04-22

Peptides

Formate dehydrogenase subunit alpha: AE
Formate dehydrogenase subunit beta: BF
Formate dehydrogenase subunit gamma: CG
NAD-dependent formate dehydrogenase subunit delta: DH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
G

G
C

D
D

H
H

Formate dehydrogenase subunit alpha

Formate dehydrogenase subunit beta

Formate dehydrogenase subunit gamma

NAD-dependent formate dehydrogenase subunit delta

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