SMTL ID : 5t5m.1

TUNGSTEN-CONTAINING FORMYLMETHANOFURAN DEHYDROGENASE FROM METHANOTHERMOBACTER WOLFEII, TRIGONAL FORM AT 2.5 A.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-2-2-2-2-mer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: V.340, T.344 Chain B: E.138, R.142 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:T.344, B:E.138, H2O.2 MG.4: 4 residues within 4Å: Chain A: R.69, R.72, S.76 Chain B: G.305 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:G.305, A:R.69, A:S.76, H2O.1, H2O.3 MG.13: 6 residues within 4Å: Chain B: D.128 Chain C: S.139, Y.140, G.142, D.143, Y.165 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.139, C:Y.140, C:D.143, H2O.5, H2O.6 MG.25: 4 residues within 4Å: Chain G: V.340, T.344 Chain H: E.138, R.142 3 PLIP interactions: 1 interactions with chain G, 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: G:T.344, H:E.138, H2O.12 MG.28: 4 residues within 4Å: Chain G: R.69, R.72, S.76 Chain H: G.305 5 PLIP interactions: 1 interactions with chain H, 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: H:G.305, G:R.69, G:S.76, H2O.11, H2O.13 MG.37: 6 residues within 4Å: Chain H: D.128 Chain I: S.139, Y.140, G.142, D.143, Y.165 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:S.139, I:Y.140, I:D.143, H2O.15, H2O.16

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: K.178, H.231, H.271 Ligands: ZN.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.231, A:H.271, H2O.1 ZN.3: 5 residues within 4Å: Chain A: H.57, H.59, K.178, D.385 Ligands: ZN.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.57, A:H.59, A:D.385, H2O.1 ZN.26: 4 residues within 4Å: Chain G: K.178, H.231, H.271 Ligands: ZN.27 3 PLIP interactions: 2 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:H.231, G:H.271, H2O.11 ZN.27: 5 residues within 4Å: Chain G: H.57, H.59, K.178, D.385 Ligands: ZN.26 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:H.57, G:H.59, G:D.385, H2O.11

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: W.190, G.191 Chain B: N.277, D.278, Y.279 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.279, A:G.191 GOL.6: 5 residues within 4Å: Chain A: K.77 Chain C: R.78, Q.81, E.82, D.120 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.78, A:K.77 GOL.14: 3 residues within 4Å: Chain D: Y.57, R.89, Y.91 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.57, D:R.89 GOL.29: 5 residues within 4Å: Chain G: W.190, G.191 Chain H: N.277, D.278, Y.279 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:G.191, H:Y.279 GOL.30: 5 residues within 4Å: Chain G: K.77 Chain I: R.78, Q.81, E.82, D.120 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain G Hydrogen bonds: I:R.78, I:D.120, G:K.77 GOL.38: 3 residues within 4Å: Chain J: Y.57, R.89, Y.91 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:Y.57, J:Y.57, J:R.89

2 x K: POTASSIUM ION(Non-covalent)

K.7: 6 residues within 4Å: Chain B: S.40, V.43, H.44, A.45 Chain D: E.18, S.19 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Metal complexes: D:E.18, B:V.43 K.31: 6 residues within 4Å: Chain H: S.40, V.43, H.44, A.45 Chain J: E.18, S.19 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain H Metal complexes: J:E.18, H:V.43

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

SF4.8: 9 residues within 4Å: Chain B: C.9, F.11, C.12, T.14, L.15, C.16, C.35, G.38, R.159 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.9, B:C.12, B:C.16, B:C.35 SF4.15: 9 residues within 4Å: Chain E: C.154, I.155, Y.156, C.157, G.158, C.160, C.204, P.205, I.209 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.154, E:C.157, E:C.160, E:C.204 SF4.16: 11 residues within 4Å: Chain E: I.147, C.164, P.165, V.166, I.169, C.194, V.195, H.196, C.197, G.198, C.200 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.164, E:C.194, E:C.197, E:C.200 SF4.17: 10 residues within 4Å: Chain E: L.264, C.281, P.282, V.285, C.308, I.309, Y.310, C.311, G.312, C.314 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.281, E:C.308, E:C.311, E:C.314 SF4.18: 12 residues within 4Å: Chain E: C.271, Q.272, A.273, C.274, E.275, T.276, C.277, L.301, C.318, V.320, A.322, I.323 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.271, E:C.274, E:C.277, E:C.318 SF4.19: 8 residues within 4Å: Chain E: L.24, C.41, I.46, C.71, L.73, C.74, G.75, C.77 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.41, E:C.71, E:C.74, E:C.77 SF4.20: 10 residues within 4Å: Chain E: C.31, A.32, V.33, C.34, G.35, C.37, C.81, F.83, A.85, L.86 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.31, E:C.34, E:C.37, E:C.81 SF4.21: 9 residues within 4Å: Chain E: C.125, I.130, C.239, V.240, N.241, C.242, G.243, C.245, V.256 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.125, E:C.239, E:C.242, E:C.245 SF4.22: 9 residues within 4Å: Chain E: C.115, I.116, Q.117, C.118, K.119, C.121, C.249, P.250, V.251 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.115, E:C.118, E:C.121, E:C.249 SF4.23: 10 residues within 4Å: Chain F: C.12, H.13, G.14, C.15, G.16, C.18, C.71, V.73, A.75, I.76 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.12, F:C.15, F:C.18, F:C.71 SF4.24: 9 residues within 4Å: Chain F: C.22, I.45, M.46, C.61, G.62, K.63, C.64, G.65, C.67 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.22, F:C.61, F:C.64, F:C.67 SF4.32: 9 residues within 4Å: Chain H: C.9, F.11, C.12, T.14, L.15, C.16, C.35, G.38, R.159 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.9, H:C.12, H:C.16, H:C.35 SF4.39: 9 residues within 4Å: Chain K: C.154, I.155, Y.156, C.157, G.158, C.160, C.204, P.205, I.209 4 PLIP interactions: 4 interactions with chain K, Metal complexes: K:C.154, K:C.157, K:C.160, K:C.204 SF4.40: 11 residues within 4Å: Chain K: I.147, C.164, P.165, V.166, I.169, C.194, V.195, H.196, C.197, G.198, C.200 4 PLIP interactions: 4 interactions with chain K, Metal complexes: K:C.164, K:C.194, K:C.197, K:C.200 SF4.41: 10 residues within 4Å: Chain K: L.264, C.281, P.282, V.285, C.308, I.309, Y.310, C.311, G.312, C.314 4 PLIP interactions: 4 interactions with chain K, Metal complexes: K:C.281, K:C.308, K:C.311, K:C.314 SF4.42: 12 residues within 4Å: Chain K: C.271, Q.272, A.273, C.274, E.275, T.276, C.277, L.301, C.318, V.320, A.322, I.323 4 PLIP interactions: 4 interactions with chain K, Metal complexes: K:C.271, K:C.274, K:C.277, K:C.318 SF4.43: 8 residues within 4Å: Chain K: L.24, C.41, I.46, C.71, L.73, C.74, G.75, C.77 4 PLIP interactions: 4 interactions with chain K, Metal complexes: K:C.41, K:C.71, K:C.74, K:C.77 SF4.44: 10 residues within 4Å: Chain K: C.31, A.32, V.33, C.34, G.35, C.37, C.81, F.83, A.85, L.86 4 PLIP interactions: 4 interactions with chain K, Metal complexes: K:C.31, K:C.34, K:C.37, K:C.81 SF4.45: 9 residues within 4Å: Chain K: C.125, I.130, C.239, V.240, N.241, C.242, G.243, C.245, V.256 4 PLIP interactions: 4 interactions with chain K, Metal complexes: K:C.125, K:C.239, K:C.242, K:C.245 SF4.46: 9 residues within 4Å: Chain K: C.115, I.116, Q.117, C.118, K.119, C.121, C.249, P.250, V.251 4 PLIP interactions: 4 interactions with chain K, Metal complexes: K:C.115, K:C.118, K:C.121, K:C.249 SF4.47: 10 residues within 4Å: Chain L: C.12, H.13, G.14, C.15, G.16, C.18, C.71, V.73, A.75, I.76 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:C.12, L:C.15, L:C.18, L:C.71 SF4.48: 9 residues within 4Å: Chain L: C.22, I.45, M.46, C.61, G.62, K.63, C.64, G.65, C.67 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:C.22, L:C.61, L:C.64, L:C.67

2 x W: TUNGSTEN ION(Non-covalent)

W.9: 5 residues within 4Å: Chain B: C.118 Chain D: R.9 Ligands: MGD.10, MGD.11, H2S.12 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.118 W.33: 5 residues within 4Å: Chain H: C.118 Chain J: R.9 Ligands: MGD.34, MGD.35, H2S.36 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:C.118

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.10: 34 residues within 4Å: Chain B: K.41, C.91, T.114, V.117, C.118, M.254, H.258, H.290, A.342, S.343, D.344, H.348, I.365, E.366, P.367, H.368, T.370, P.382, A.383, I.384, V.385, D.414 Chain D: T.7, G.8, R.9, E.18, K.21, M.80, N.85, F.100, K.101 Ligands: W.9, MGD.11, H2S.12 25 PLIP interactions: 11 interactions with chain D, 14 interactions with chain B Hydrogen bonds: D:T.7, D:T.7, D:R.9, D:R.9, D:K.21, D:K.21, D:N.85, D:N.85, D:K.101, B:K.41, B:A.342, B:D.344, B:H.348, B:I.365, B:V.385 Salt bridges: D:K.21, B:H.290, B:H.290, B:H.348, B:H.348, B:D.414 pi-Stacking: D:F.100 Water bridges: B:Y.87, B:Y.87, B:T.370 MGD.11: 36 residues within 4Å: Chain B: F.11, I.37, G.150, C.151, N.152, H.155, A.156, H.157, V.184, D.185, P.186, R.187, T.189, L.201, F.203, D.204, D.206, G.253, M.254, G.255, S.259, G.289, H.290 Chain D: N.6, G.8, R.9, T.10, Q.13, G.14, I.17, M.80, K.101, N.102 Ligands: W.9, MGD.10, H2S.12 26 PLIP interactions: 11 interactions with chain D, 15 interactions with chain B Hydrogen bonds: D:N.6, D:R.9, D:R.9, D:Q.13, D:Q.13, D:G.14, D:N.102, B:N.152, B:H.155, B:A.156, B:V.184, B:R.187, B:R.187, B:D.204, B:M.254, B:S.259 Water bridges: D:Y.77, B:N.152, B:H.157, B:D.206 Salt bridges: D:R.9, D:R.9, D:K.101, B:D.185, B:D.206 pi-Stacking: B:F.11 MGD.34: 34 residues within 4Å: Chain H: K.41, C.91, T.114, V.117, C.118, M.254, H.258, H.290, A.342, S.343, D.344, H.348, I.365, E.366, P.367, H.368, T.370, P.382, A.383, I.384, V.385, D.414 Chain J: T.7, G.8, R.9, E.18, K.21, M.80, N.85, F.100, K.101 Ligands: W.33, MGD.35, H2S.36 25 PLIP interactions: 14 interactions with chain H, 11 interactions with chain J Hydrogen bonds: H:K.41, H:H.258, H:A.342, H:D.344, H:H.348, H:I.365, H:V.385, J:T.7, J:T.7, J:R.9, J:R.9, J:K.21, J:K.21, J:N.85, J:N.85, J:K.101 Water bridges: H:Y.291, H:Y.291 Salt bridges: H:H.290, H:H.290, H:H.348, H:H.348, H:D.414, J:K.21 pi-Stacking: J:F.100 MGD.35: 36 residues within 4Å: Chain H: F.11, I.37, G.150, C.151, N.152, H.155, A.156, H.157, V.184, D.185, P.186, R.187, T.189, L.201, F.203, D.204, D.206, G.253, M.254, G.255, S.259, G.289, H.290 Chain J: N.6, G.8, R.9, T.10, Q.13, G.14, I.17, M.80, K.101, N.102 Ligands: W.33, MGD.34, H2S.36 26 PLIP interactions: 15 interactions with chain H, 11 interactions with chain J Hydrogen bonds: H:N.152, H:H.155, H:A.156, H:V.184, H:R.187, H:R.187, H:D.204, H:D.204, H:M.254, H:S.259, J:N.6, J:R.9, J:R.9, J:Q.13, J:Q.13, J:G.14, J:N.102 Water bridges: H:N.152, H:D.206, J:Y.77 Salt bridges: H:D.185, H:D.206, J:R.9, J:R.9, J:K.101 pi-Stacking: H:F.11

2 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.12: 7 residues within 4Å: Chain B: T.114, C.118, G.289, H.290 Ligands: W.9, MGD.10, MGD.11 No protein-ligand interaction detected (PLIP) H2S.36: 7 residues within 4Å: Chain H: T.114, C.118, G.289, H.290 Ligands: W.33, MGD.34, MGD.35 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wagner, T. et al., The methanogenic CO2 reducing-and-fixing enzyme is bifunctional and contains 46 [4Fe-4S] clusters. Science (2016)

Release Date

2016-10-19

Peptides

Tungsten formylmethanofuran dehydrogenase subunit fwdA: AG
Tungsten formylmethanofuran dehydrogenase subunit fwdB: BH
Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C: CI
Tungsten formylmethanofuran dehydrogenase subunit fwdD: DJ
Tungsten formylmethanofuran dehydrogenase subunit fwdF: EK
Tungsten formylmethanofuran dehydrogenase subunit fwdG: FL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

G
A

B
B

H
B

C
C

I
C

D
D

J
D

E
F

K
F

F
G

L
G

Tungsten formylmethanofuran dehydrogenase subunit fwdA

Tungsten formylmethanofuran dehydrogenase subunit fwdB

Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C

Tungsten formylmethanofuran dehydrogenase subunit fwdD

Tungsten formylmethanofuran dehydrogenase subunit fwdF

Tungsten formylmethanofuran dehydrogenase subunit fwdG

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