SMTL ID : 7z0s.1

Structure of the Escherichia coli formate hydrogenlyase complex (anaerobic preparation, without formate dehydrogenase H)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.1: 20 residues within 4Å: Chain A: L.153, A.156, L.157, I.212, P.213, L.214, H.215, G.216, Q.220, I.269, V.273, Y.277, Y.290, R.567, L.570, N.571, P.572, V.573, V.576, W.579 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.153, A:A.156, A:I.212, A:P.213, A:P.213, A:L.214, A:I.269, A:L.570, A:P.572, A:W.579 Hydrogen bonds: A:Q.220, A:Y.290, A:N.571 Salt bridges: A:H.215, A:H.215, A:R.567

2 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.2: 17 residues within 4Å: Chain A: V.265, M.268, I.269, F.272, L.412, L.415, V.418, G.419, I.422, Q.558, A.559, F.560, A.561, P.562, V.563 Chain F: W.291, F.294 17 PLIP interactions: 12 interactions with chain A, 5 interactions with chain F Hydrophobic interactions: A:M.268, A:I.269, A:F.272, A:F.272, A:F.272, A:F.272, A:L.412, A:L.415, A:V.418, A:I.422, A:F.560, A:V.563, F:W.291, F:W.291, F:W.291, F:W.291, F:F.294 PTY.3: 14 residues within 4Å: Chain A: M.377, L.382, P.383, P.384, L.385, L.507, F.515, S.528 Chain F: W.62, R.65, L.66, Y.69, I.106, F.110 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain F Hydrophobic interactions: A:L.382, A:L.385, A:L.507, A:F.515, F:Y.69, F:I.106, F:F.110 Hydrogen bonds: A:S.528, A:S.528, F:R.65 Water bridges: F:S.54, F:S.54

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

NI.4: 5 residues within 4Å: Chain B: C.253, C.256, C.543, C.546 Ligands: FCO.5 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.5: 12 residues within 4Å: Chain B: C.256, H.260, A.488, P.489, R.490, D.493, A.512, A.513, T.514, C.543, C.546 Ligands: NI.4 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.490, B:R.490, B:A.513, B:T.514, B:T.514 Metal complexes: B:C.256, B:C.546

1 x DR9: 1-CIS-9-OCTADECANOYL-2-CIS-9-HEXADECANOYL PHOSPHATIDYL GLYCEROL(Non-covalent)

DR9.6: 18 residues within 4Å: Chain B: S.377, T.378, P.379, N.380 Chain F: A.183, F.184, F.187, P.194, F.235, I.240, K.263, V.266, G.267, V.270, I.271, F.274, M.278, I.289 15 PLIP interactions: 14 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: F:F.184, F:F.187, F:F.187, F:P.194, F:F.235, F:I.240, F:V.266, F:V.270, F:I.271, F:F.274, F:F.274, F:F.274, F:F.274, F:F.274 Hydrogen bonds: B:T.378

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

SF4.7: 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 SF4.8: 13 residues within 4Å: Chain C: V.5, 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 SF4.9: 13 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, A.96, 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 SF4.10: 13 residues within 4Å: Chain C: C.63, P.64, V.65, 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 SF4.11: 11 residues within 4Å: Chain B: R.251 Chain D: G.47, C.48, G.50, C.51, G.113, A.114, C.115, G.144, C.145, P.146 5 PLIP interactions: 5 interactions with chain D, Salt bridges: D:E.52 Metal complexes: D:C.48, D:C.51, D:C.115, D:C.145 SF4.12: 14 residues within 4Å: Chain E: Q.35, C.40, I.41, G.42, C.43, A.44, A.45, C.46, W.68, C.85, P.86, T.87, A.89, I.90 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.40, E:C.43, E:C.46, E:C.85 SF4.13: 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

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

FE.14: 4 residues within 4Å: Chain E: C.117, 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

1 x LMN: Lauryl Maltose Neopentyl Glycol(Non-covalent)

LMN.15: 8 residues within 4Å: Chain F: Y.165, H.166, W.167, L.179, F.239, I.240, W.242, E.246 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:W.167, F:W.167, F:I.240, F:I.240, F:W.242, F:W.242, F:W.242 Hydrogen bonds: F:W.167

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
E

C
B

D
G

E
F

F
D

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

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