SMTL ID : 7z0t.1

Structure of the Escherichia coli formate hydrogenlyase complex (aerobic preparation, composite structure)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 5 residues within 4Å: Chain B: C.253, C.256, C.543, C.546 Ligands: FCO.2 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.253, B:C.256, B:C.543, B:C.546

1 x FCO: CARBONMONOXIDE-(DICYANO) IRON(Non-covalent)

FCO.2: 13 residues within 4Å: Chain B: C.253, C.256, H.260, A.488, P.489, R.490, D.493, A.512, A.513, T.514, C.543, C.546 Ligands: NI.1 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.260, B:R.490, B:A.513, B:T.514 Metal complexes: B:C.256, B:C.546

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

SF4.3: 14 residues within 4Å: Chain C: C.12, I.13, G.14, C.15, H.16, T.17, C.18, V.39, P.48, C.159, P.160, T.161, A.163, L.164 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.12, C:C.15, C:C.18, C:C.159 SF4.4: 12 residues within 4Å: Chain C: C.22, H.26, R.36, L.37, L.50, C.143, D.144, L.145, C.146, P.153, A.154, C.155 5 PLIP interactions: 5 interactions with chain C, Salt bridges: C:D.144 Metal complexes: C:C.22, C:C.143, C:C.146, C:C.155 SF4.5: 12 residues within 4Å: Chain C: C.51, H.52, H.53, C.54, P.58, C.59, V.75, C.92, P.93, F.94, I.97, K.142 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.51, C:C.54, C:C.59, C:C.92 SF4.6: 14 residues within 4Å: Chain C: C.63, P.64, V.65, A.67, I.68, L.77, C.82, V.83, C.85, K.86, L.87, C.88, F.99, A.140 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.63, C:C.82, C:C.85, C:C.88 SF4.7: 8 residues within 4Å: Chain D: G.47, C.48, C.51, G.113, A.114, C.115, G.144, C.145 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.48, D:C.51, D:C.115, D:C.145 SF4.8: 11 residues within 4Å: Chain E: C.40, I.41, C.43, A.45, C.46, W.68, C.85, P.86, T.87, A.89, I.90 5 PLIP interactions: 5 interactions with chain E, Metal complexes: E:C.40, E:C.43, E:C.43, E:C.46, E:C.85 SF4.9: 13 residues within 4Å: Chain E: C.50, P.51, S.52, A.54, L.55, F.70, C.75, I.76, F.77, C.78, G.79, R.80, C.81 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.50, E:C.75, E:C.78, E:C.81 SF4.11: 11 residues within 4Å: Chain G: C.8, Y.10, C.11, S.13, C.15, L.41, C.42, K.44, G.45, P.182, I.183 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.8, G:C.11, G:C.15, G:C.42

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

FE.10: 5 residues within 4Å: Chain E: C.117, V.119, C.120, C.155, C.158 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.117, E:C.120, E:C.155, E:C.158

2 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.12: 34 residues within 4Å: Chain G: R.110, G.111, T.112, C.136, V.139, U.140, M.297, Q.301, Q.335, G.402, E.403, D.404, T.408, Q.428, D.429, I.430, F.431, T.433, S.445, T.446, W.448, H.451, D.478, T.579, R.581, S.587, C.588, S.590, Y.654, N.662, Y.678, K.679 Ligands: MGD.13, 6MO.14 24 PLIP interactions: 24 interactions with chain G Hydrogen bonds: G:Q.301, G:Q.335, G:D.404, G:T.408, G:Q.428, G:D.429, G:I.430, G:S.445, G:T.579, G:R.581, G:R.581, G:S.587, G:S.587, G:S.590, G:Y.654, G:N.662, G:N.662, G:K.679 Salt bridges: G:R.110, G:D.478 pi-Stacking: G:Y.654, G:Y.678 pi-Cation interactions: G:Y.654, G:Y.678 MGD.13: 37 residues within 4Å: Chain G: K.44, U.140, G.174, Y.175, N.176, D.179, S.180, H.181, C.201, D.202, P.203, R.204, I.206, L.218, N.220, G.221, N.223, G.296, M.297, G.298, F.302, G.334, Q.335, S.578, V.580, R.581, E.582, V.583, H.585, Y.586, S.587, Y.651, Y.654, Q.655, K.679 Ligands: MGD.12, 6MO.14 20 PLIP interactions: 20 interactions with chain G Hydrogen bonds: G:N.176, G:S.180, G:S.180, G:S.180, G:D.202, G:R.204, G:G.221, G:N.223, G:N.223, G:M.297, G:S.578, G:R.581, G:H.585, G:Y.586, G:S.587, G:Q.655 Salt bridges: G:R.581, G:R.581, G:K.679 pi-Stacking: G:Y.586

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

6MO.14: 4 residues within 4Å: Chain G: U.140, G.334 Ligands: MGD.12, MGD.13 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Steinhilper, R. et al., Structure of the membrane-bound formate hydrogenlyase complex from Escherichia coli. Nat Commun (2022)

Release Date

2022-09-28

Peptides

Formate hydrogenlyase subunit 3: A
Formate hydrogenlyase subunit 5: B
Formate hydrogenlyase subunit 2: C
Formate hydrogenlyase subunit 7: D
Formate hydrogenlyase subunit 6: E
Formate hydrogenlyase subunit 4: F
Formate dehydrogenase H: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
E

C
B

D
G

E
F

F
D

G
A

Membrane

We predict this structure to be a membrane protein.
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Formate hydrogenlyase subunit 3

Formate hydrogenlyase subunit 5

Formate hydrogenlyase subunit 2

Formate hydrogenlyase subunit 7

Formate hydrogenlyase subunit 6

Formate hydrogenlyase subunit 4

Formate dehydrogenase H

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