SMTL ID : 7qv7.1

Cryo-EM structure of Hydrogen-dependent CO2 reductase.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-6-6-2-mer

Ligands

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

SF4.1: 11 residues within 4Å: Chain A: C.13, L.14, G.15, C.16, Y.17, T.18, C.19, P.49, C.149, P.150, L.154 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.13, A:C.16, A:C.19, A:C.149 SF4.2: 9 residues within 4Å: Chain A: C.52, R.53, C.55, P.59, C.60, C.93, F.95, I.98, K.132 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.52, A:C.55, A:C.60, A:C.93 SF4.3: 11 residues within 4Å: Chain A: C.64, P.65, V.66, I.69, I.78, C.83, I.84, G.85, C.86, C.89, F.100 5 PLIP interactions: 5 interactions with chain A, Metal complexes: A:C.64, A:C.83, A:C.86, A:C.86, A:C.89 SF4.4: 10 residues within 4Å: Chain A: C.23, H.27, L.38, C.133, D.134, L.135, C.136, P.143, A.144, C.145 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:D.134 Metal complexes: A:C.23, A:C.133, A:C.136, A:C.145 SF4.5: 13 residues within 4Å: Chain B: C.34, I.35, G.36, C.37, K.38, A.39, C.40, L.71, P.80, C.180, P.181, E.182, L.185 5 PLIP interactions: 5 interactions with chain B, Salt bridges: B:E.182 Metal complexes: B:C.34, B:C.37, B:C.40, B:C.180 SF4.6: 11 residues within 4Å: Chain B: C.83, R.84, H.85, C.86, A.89, P.90, C.91, I.107, C.124, F.126, I.129 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.83, B:C.86, B:C.91, B:C.124 SF4.7: 8 residues within 4Å: Chain B: C.95, A.99, I.100, C.114, I.115, C.117, S.119, C.120 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.95, B:C.114, B:C.117, B:C.120 SF4.8: 11 residues within 4Å: Chain B: C.44, H.48, R.68, L.69, C.165, D.166, L.167, C.168, P.174, A.175, C.176 5 PLIP interactions: 5 interactions with chain B, Metal complexes: B:C.44, B:H.48, B:C.165, B:C.168, B:C.176 SF4.9: 11 residues within 4Å: Chain C: C.34, I.35, G.36, C.37, K.38, A.39, C.40, L.71, C.180, P.181, E.182 6 PLIP interactions: 6 interactions with chain C, Salt bridges: C:E.182, C:E.182 Metal complexes: C:C.34, C:C.37, C:C.40, C:C.180 SF4.10: 10 residues within 4Å: Chain C: C.83, R.84, H.85, C.86, P.90, C.91, I.107, C.124, F.126, I.129 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.83, C:C.86, C:C.91, C:C.124 SF4.11: 10 residues within 4Å: Chain C: C.95, A.99, I.100, V.109, C.114, I.115, G.116, C.117, S.119, C.120 5 PLIP interactions: 5 interactions with chain C, Metal complexes: C:C.95, C:C.114, C:C.117, C:C.117, C:C.120 SF4.12: 10 residues within 4Å: Chain C: C.44, H.48, L.69, C.165, D.166, L.167, C.168, P.174, A.175, C.176 5 PLIP interactions: 5 interactions with chain C, Salt bridges: C:D.166 Metal complexes: C:C.44, C:C.165, C:C.168, C:C.176 SF4.13: 9 residues within 4Å: Chain D: I.10, C.15, T.16, G.17, C.18, R.19, C.21, K.54, C.55 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.15, D:C.18, D:C.21, D:C.55 SF4.14: 10 residues within 4Å: Chain D: C.25, P.26, V.27, A.29, I.40, C.45, V.46, C.48, G.49, C.51 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.25, D:C.45, D:C.48, D:C.51 SF4.16: 12 residues within 4Å: Chain D: C.184, A.186, P.238, C.239, C.241, K.242, T.382, C.383, G.386, C.387, G.390 Ligands: 402.15 5 PLIP interactions: 5 interactions with chain D, Metal complexes: D:C.184, D:C.239, D:C.241, D:C.383, D:C.387 SF4.17: 10 residues within 4Å: Chain E: C.13, L.14, G.15, C.16, Y.17, C.19, P.49, C.149, P.150, L.154 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.13, E:C.16, E:C.19, E:C.149 SF4.18: 9 residues within 4Å: Chain E: C.52, R.53, C.55, A.58, C.60, C.93, F.95, I.98, K.132 5 PLIP interactions: 5 interactions with chain E, Metal complexes: E:C.52, E:C.55, E:A.58, E:C.60, E:C.93 SF4.19: 10 residues within 4Å: Chain E: C.64, V.66, I.69, I.78, C.83, I.84, G.85, C.86, C.89, F.100 5 PLIP interactions: 5 interactions with chain E, Metal complexes: E:C.64, E:C.83, E:C.86, E:C.86, E:C.89 SF4.20: 11 residues within 4Å: Chain E: C.23, H.27, R.37, L.38, C.133, D.134, L.135, C.136, P.143, A.144, C.145 5 PLIP interactions: 5 interactions with chain E, Salt bridges: E:D.134 Metal complexes: E:C.23, E:C.133, E:C.136, E:C.145 SF4.21: 12 residues within 4Å: Chain F: C.34, I.35, G.36, C.37, K.38, C.40, L.71, P.80, C.180, P.181, E.182, L.185 5 PLIP interactions: 5 interactions with chain F, Salt bridges: F:E.182 Metal complexes: F:C.34, F:C.37, F:C.40, F:C.180 SF4.22: 10 residues within 4Å: Chain F: C.83, R.84, C.86, A.89, P.90, C.91, I.107, C.124, F.126, I.129 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.83, F:C.86, F:C.91, F:C.124 SF4.23: 10 residues within 4Å: Chain F: C.95, A.99, I.100, V.109, C.114, I.115, G.116, C.117, S.119, C.120 5 PLIP interactions: 5 interactions with chain F, Metal complexes: F:C.95, F:C.114, F:C.117, F:C.117, F:C.120 SF4.24: 10 residues within 4Å: Chain F: C.44, H.48, L.69, C.165, D.166, L.167, C.168, P.174, A.175, C.176 5 PLIP interactions: 5 interactions with chain F, Salt bridges: F:D.166 Metal complexes: F:C.44, F:C.165, F:C.168, F:C.176 SF4.25: 10 residues within 4Å: Chain G: I.10, C.15, G.17, C.18, R.19, R.20, C.21, Q.38, K.54, C.55 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.15, G:C.18, G:C.21, G:C.55 SF4.26: 11 residues within 4Å: Chain G: C.25, P.26, V.27, A.29, I.40, C.45, V.46, M.47, C.48, G.49, C.51 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.25, G:C.45, G:C.48, G:C.51 SF4.28: 11 residues within 4Å: Chain G: C.184, P.185, A.186, P.238, C.239, C.241, K.242, M.381, C.383, C.387 Ligands: 402.27 5 PLIP interactions: 5 interactions with chain G, Metal complexes: G:C.184, G:C.239, G:C.241, G:C.383, G:C.387 SF4.29: 12 residues within 4Å: Chain H: C.34, I.35, G.36, C.37, K.38, C.40, L.71, C.180, P.181, E.182, A.184, L.185 5 PLIP interactions: 5 interactions with chain H, Salt bridges: H:E.182 Metal complexes: H:C.34, H:C.37, H:C.40, H:C.180 SF4.30: 11 residues within 4Å: Chain H: C.83, R.84, H.85, C.86, A.89, P.90, C.91, I.107, C.124, I.129, K.164 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.83, H:C.86, H:C.91, H:C.124 SF4.31: 10 residues within 4Å: Chain H: C.95, V.97, I.100, C.114, I.115, G.116, C.117, S.119, C.120, L.131 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.95, H:C.114, H:C.117, H:C.120 SF4.32: 10 residues within 4Å: Chain H: C.44, H.48, L.69, C.165, D.166, L.167, C.168, P.174, A.175, C.176 5 PLIP interactions: 5 interactions with chain H, Salt bridges: H:D.166 Metal complexes: H:C.44, H:C.165, H:C.168, H:C.176 SF4.33: 12 residues within 4Å: Chain I: C.34, I.35, G.36, C.37, K.38, A.39, C.40, L.71, C.180, P.181, E.182, L.185 5 PLIP interactions: 5 interactions with chain I, Salt bridges: I:E.182 Metal complexes: I:C.34, I:C.37, I:C.40, I:C.180 SF4.34: 8 residues within 4Å: Chain I: C.83, R.84, C.86, P.90, C.91, C.124, F.126, K.164 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.83, I:C.86, I:C.91, I:C.124 SF4.35: 9 residues within 4Å: Chain I: C.95, A.99, I.100, C.114, I.115, C.117, S.119, C.120, L.131 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.95, I:C.114, I:C.117, I:C.120 SF4.36: 10 residues within 4Å: Chain I: C.44, H.48, L.69, C.165, D.166, L.167, C.168, P.174, A.175, C.176 5 PLIP interactions: 5 interactions with chain I, Salt bridges: I:D.166 Metal complexes: I:C.44, I:C.165, I:C.168, I:C.176 SF4.37: 11 residues within 4Å: Chain J: I.10, C.15, T.16, C.18, R.19, R.20, C.21, Q.38, K.54, C.55, A.88 4 PLIP interactions: 4 interactions with chain J, Metal complexes: J:C.15, J:C.18, J:C.21, J:C.55 SF4.38: 11 residues within 4Å: Chain J: C.25, P.26, V.27, A.29, I.40, C.45, V.46, C.48, G.49, Q.50, C.51 4 PLIP interactions: 4 interactions with chain J, Metal complexes: J:C.25, J:C.45, J:C.48, J:C.51 SF4.39: 10 residues within 4Å: Chain J: C.48, C.184, P.238, C.239, C.241, K.242, M.381, C.383, C.387 Ligands: 402.40 5 PLIP interactions: 5 interactions with chain J, Metal complexes: J:C.184, J:C.239, J:C.241, J:C.383, J:C.387 SF4.41: 11 residues within 4Å: Chain K: I.10, C.15, T.16, G.17, C.18, R.19, C.21, Q.38, K.54, C.55, S.57 4 PLIP interactions: 4 interactions with chain K, Metal complexes: K:C.15, K:C.18, K:C.21, K:C.55 SF4.42: 8 residues within 4Å: Chain K: I.8, C.25, I.40, C.45, V.46, C.48, G.49, C.51 4 PLIP interactions: 4 interactions with chain K, Metal complexes: K:C.25, K:C.45, K:C.48, K:C.51 SF4.44: 9 residues within 4Å: Chain K: C.184, P.185, A.186, C.239, C.241, T.382, C.383, C.387 Ligands: 402.43 5 PLIP interactions: 5 interactions with chain K, Metal complexes: K:C.184, K:C.239, K:C.241, K:C.383, K:C.387 SF4.45: 10 residues within 4Å: Chain L: C.13, Y.15, C.16, G.19, C.20, L.47, C.48, K.50, G.51, L.183 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:C.13, L:C.16, L:C.20, L:C.48 SF4.46: 10 residues within 4Å: Chain M: I.10, C.15, T.16, G.17, C.18, R.19, C.21, Q.38, C.55, S.57 4 PLIP interactions: 4 interactions with chain M, Metal complexes: M:C.15, M:C.18, M:C.21, M:C.55 SF4.47: 9 residues within 4Å: Chain M: C.25, I.30, I.40, C.45, M.47, C.48, G.49, Q.50, C.51 4 PLIP interactions: 4 interactions with chain M, Metal complexes: M:C.25, M:C.45, M:C.48, M:C.51 SF4.49: 9 residues within 4Å: Chain M: C.184, P.185, A.186, C.239, C.241, T.382, C.383, C.387 Ligands: 402.48 5 PLIP interactions: 5 interactions with chain M, Metal complexes: M:C.184, M:C.239, M:C.241, M:C.383, M:C.387 SF4.50: 11 residues within 4Å: Chain N: C.34, I.35, G.36, C.37, K.38, A.39, C.40, L.71, P.80, C.180, L.185 5 PLIP interactions: 5 interactions with chain N, Salt bridges: N:E.182 Metal complexes: N:C.34, N:C.37, N:C.40, N:C.180 SF4.51: 11 residues within 4Å: Chain N: C.83, R.84, H.85, C.86, A.89, P.90, C.91, C.124, F.126, I.129, K.164 4 PLIP interactions: 4 interactions with chain N, Metal complexes: N:C.83, N:C.86, N:C.91, N:C.124 SF4.52: 6 residues within 4Å: Chain N: C.95, C.114, I.115, G.116, C.117, C.120 5 PLIP interactions: 5 interactions with chain N, Metal complexes: N:C.95, N:C.114, N:C.117, N:C.117, N:C.120 SF4.53: 10 residues within 4Å: Chain N: C.44, H.48, L.69, C.165, D.166, L.167, C.168, P.174, A.175, C.176 5 PLIP interactions: 5 interactions with chain N, Salt bridges: N:D.166 Metal complexes: N:C.44, N:C.165, N:C.168, N:C.176 SF4.54: 9 residues within 4Å: Chain O: C.13, Y.15, C.16, G.19, C.20, L.47, C.48, K.50, G.51 4 PLIP interactions: 4 interactions with chain O, Metal complexes: O:C.13, O:C.16, O:C.20, O:C.48 SF4.55: 10 residues within 4Å: Chain P: I.10, C.15, T.16, G.17, C.18, R.19, C.21, Q.38, K.54, C.55 4 PLIP interactions: 4 interactions with chain P, Metal complexes: P:C.15, P:C.18, P:C.21, P:C.55 SF4.56: 8 residues within 4Å: Chain P: C.25, P.26, C.45, V.46, M.47, C.48, G.49, C.51 4 PLIP interactions: 4 interactions with chain P, Metal complexes: P:C.25, P:C.45, P:C.48, P:C.51 SF4.57: 10 residues within 4Å: Chain P: C.183, C.184, P.185, A.186, C.239, C.241, K.242, C.383, C.387 Ligands: 402.58 5 PLIP interactions: 5 interactions with chain P, Metal complexes: P:C.184, P:C.239, P:C.241, P:C.383, P:C.387

6 x 402: dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)(Covalent)(Non-covalent)

402.15: 13 residues within 4Å: Chain D: A.114, A.116, T.152, C.183, C.184, Q.209, M.237, C.239, K.242, F.301, G.302, C.387 Ligands: SF4.16 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.152, D:K.242 Metal complexes: D:C.387 402.27: 13 residues within 4Å: Chain G: A.114, P.115, A.116, T.152, C.183, P.208, Q.209, M.237, C.239, K.242, F.301, C.387 Ligands: SF4.28 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:Q.209, G:K.242 Metal complexes: G:C.387 402.40: 13 residues within 4Å: Chain J: A.114, P.115, A.116, T.152, C.183, M.237, P.238, C.239, K.242, F.301, G.302, C.387 Ligands: SF4.39 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:C.387 402.43: 14 residues within 4Å: Chain K: P.115, A.116, T.152, C.183, S.207, P.208, Q.209, M.237, P.238, C.239, K.242, F.301, C.387 Ligands: SF4.44 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:Q.209, K:K.242 Metal complexes: K:C.387 402.48: 13 residues within 4Å: Chain M: P.115, A.116, C.183, S.207, P.208, M.237, P.238, C.239, K.242, F.301, M.381, C.387 Ligands: SF4.49 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:K.242 Metal complexes: M:C.387 402.58: 14 residues within 4Å: Chain P: P.115, A.116, T.152, C.183, S.207, P.208, Q.209, M.237, C.239, K.242, F.301, M.381, C.387 Ligands: SF4.57 3 PLIP interactions: 3 interactions with chain P Hydrogen bonds: P:Q.209, P:K.242 Metal complexes: P:C.387

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dietrich, H.M. et al., Membrane-anchored HDCR nanowires drive hydrogen-powered CO 2 fixation. Nature (2022)

Release Date

2022-07-06

Peptides

Hydrogen dependent carbon dioxide reductase subunit HycB3: AE
Hydrogen dependent carbon dioxide reductase subunit HycB4: BCFHIN
Hydrogen dependent carbon dioxide reductase subunit HydA2: DGJKMP
Hydrogen dependent carbon dioxide reductase subunit FdhF: LO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
G

B
B

C
C

F
J

H
N

I
P

N
X

D
D

G
K

J
Q

K
R

M
V

P
Z

L
S

O
Y

Hydrogen dependent carbon dioxide reductase subunit HycB3

Hydrogen dependent carbon dioxide reductase subunit HycB4

Hydrogen dependent carbon dioxide reductase subunit HydA2

Hydrogen dependent carbon dioxide reductase subunit FdhF