SMTL ID : 5t5i.1

TUNGSTEN-CONTAINING FORMYLMETHANOFURAN DEHYDROGENASE FROM METHANOTHERMOBACTER WOLFEII, ORTHORHOMBIC FORM AT 1.9 A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-oligomer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: K.178, H.231, H.271 Ligands: ZN.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.231, A:H.271, H2O.4 ZN.2: 6 residues within 4Å: Chain A: H.57, H.59, K.178, H.271, D.385 Ligands: ZN.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.57, A:H.59, A:D.385, H2O.4 ZN.36: 5 residues within 4Å: Chain G: H.57, H.59, K.178, D.385 Ligands: ZN.37 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:H.57, G:H.59, G:D.385, H2O.44 ZN.37: 4 residues within 4Å: Chain G: K.178, H.231, H.271 Ligands: ZN.36 3 PLIP interactions: 2 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:H.231, G:H.271, H2O.44

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: V.340, T.344 Chain B: E.138, R.142 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:V.340, A:T.344, B:E.138, H2O.5, H2O.6 MG.38: 4 residues within 4Å: Chain G: V.340, T.344 Chain H: E.138, R.142 5 PLIP interactions: 2 interactions with chain G, 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: G:V.340, G:T.344, H:E.138, H2O.46, H2O.51

18 x K: POTASSIUM ION(Non-covalent)

K.4: 4 residues within 4Å: Chain A: R.69, R.72, S.76 Chain B: G.305 Ligand excluded by PLIP K.5: 3 residues within 4Å: Chain A: D.264, T.265, D.300 Ligand excluded by PLIP K.16: 4 residues within 4Å: Chain B: S.40, K.41, V.43 Chain D: E.18 Ligand excluded by PLIP K.27: 4 residues within 4Å: Chain E: Q.246, E.247, C.249, D.252 Ligand excluded by PLIP K.28: 4 residues within 4Å: Chain E: E.315, R.316, C.318, T.321 Ligand excluded by PLIP K.29: 4 residues within 4Å: Chain E: E.122, T.123, C.125, D.128 Ligand excluded by PLIP K.30: 4 residues within 4Å: Chain E: E.161, E.162, C.164, D.167 Ligand excluded by PLIP K.31: 4 residues within 4Å: Chain E: K.201, R.202, C.204, D.207 Ligand excluded by PLIP K.34: 3 residues within 4Å: Chain F: V.68, C.71, D.74 Ligand excluded by PLIP K.35: 2 residues within 4Å: Chain F: N.54, I.55 Ligand excluded by PLIP K.39: 3 residues within 4Å: Chain G: D.264, T.265, D.300 Ligand excluded by PLIP K.40: 4 residues within 4Å: Chain G: R.69, R.72, S.76 Chain H: G.305 Ligand excluded by PLIP K.51: 4 residues within 4Å: Chain H: S.40, K.41, V.43 Chain J: E.18 Ligand excluded by PLIP K.63: 4 residues within 4Å: Chain K: Q.246, E.247, C.249, D.252 Ligand excluded by PLIP K.64: 4 residues within 4Å: Chain K: E.122, T.123, C.125, D.128 Ligand excluded by PLIP K.65: 3 residues within 4Å: Chain K: E.315, R.316, C.318 Ligand excluded by PLIP K.66: 4 residues within 4Å: Chain K: E.161, E.162, C.164, D.167 Ligand excluded by PLIP K.70: 3 residues within 4Å: Chain L: V.68, C.71, D.74 Ligand excluded by PLIP

5 x NA: SODIUM ION(Non-functional Binders)

NA.6: 4 residues within 4Å: Chain A: L.142, G.144, N.145, V.180 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.143, A:G.144, A:N.145, A:N.145, A:V.180, A:V.180 NA.10: 4 residues within 4Å: Chain A: I.412, E.413, G.414, L.416 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.412 Water bridges: A:Q.421 NA.41: 4 residues within 4Å: Chain G: L.142, G.144, N.145, V.180 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:F.143, G:G.144, G:N.145, G:N.145, G:V.180, G:V.180 NA.45: 4 residues within 4Å: Chain G: I.412, E.413, G.414, L.416 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:I.412 Water bridges: G:Q.421 NA.54: 4 residues within 4Å: Chain J: N.36, M.39, E.73, G.74 4 PLIP interactions: 4 interactions with chain J Hydrogen bonds: J:N.36, J:G.74 Water bridges: J:N.36, J:E.38

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: K.77 Chain C: Q.81, E.82, G.101, Q.119, D.120 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:E.82, C:Q.119, C:D.120, A:K.77 GOL.8: 5 residues within 4Å: Chain A: G.236, W.282, L.327, F.351, Q.363 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.236, A:Q.363 GOL.9: 6 residues within 4Å: Chain A: K.84, G.85, V.509, V.510, A.511, S.512 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.512 GOL.17: 5 residues within 4Å: Chain B: Y.51, F.62, R.369, T.373, E.374 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.373, B:T.373, B:E.374 GOL.42: 6 residues within 4Å: Chain G: K.77 Chain I: Q.81, E.82, G.101, Q.119, D.120 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain I Hydrogen bonds: G:K.77, I:D.120 Water bridges: I:R.78 GOL.43: 6 residues within 4Å: Chain G: V.10, N.15, V.17, M.22, L.459, G.460 2 PLIP interactions: 2 interactions with chain G Water bridges: G:L.459, G:V.461 GOL.44: 1 residues within 4Å: Chain G: Q.363 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:Q.363 Water bridges: G:Q.363 GOL.52: 6 residues within 4Å: Chain H: Y.51, F.62, R.369, T.373, E.374, I.379 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:Y.51, H:T.373 GOL.67: 7 residues within 4Å: Chain K: L.30, F.83, Q.84, Q.127, E.237, L.238, V.240 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:F.83, K:Q.84, K:Q.127

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

SF4.11: 10 residues within 4Å: Chain B: C.9, F.11, C.12, L.15, C.16, A.34, C.35, G.38, P.158, R.159 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.9, B:C.12, B:C.16, B:C.35 SF4.19: 11 residues within 4Å: Chain E: L.264, C.281, P.282, C.283, 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 SF4.20: 11 residues within 4Å: Chain E: C.271, Q.272, A.273, C.274, E.275, 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 SF4.21: 8 residues within 4Å: Chain E: C.41, I.46, C.71, V.72, 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 SF4.22: 11 residues within 4Å: Chain E: F.26, 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 SF4.23: 12 residues within 4Å: Chain E: C.125, P.126, I.130, I.234, C.239, V.240, N.241, C.242, G.243, W.244, 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 SF4.24: 12 residues within 4Å: Chain E: I.110, C.115, I.116, Q.117, C.118, K.119, C.121, I.132, C.249, P.250, V.251, A.253 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.115, E:C.118, E:C.121, E:C.249 SF4.25: 12 residues within 4Å: Chain E: C.154, I.155, Y.156, C.157, G.158, C.160, I.171, I.187, C.204, P.205, V.206, I.209 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.154, E:C.157, E:C.160, E:C.204 SF4.26: 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 SF4.32: 12 residues within 4Å: Chain F: C.12, H.13, G.14, C.15, G.16, N.17, C.18, V.53, 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 SF4.33: 14 residues within 4Å: Chain E: P.319 Chain F: L.5, C.22, P.23, V.24, I.45, M.46, C.61, G.62, K.63, C.64, G.65, T.66, C.67 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.22, F:C.61, F:C.64, F:C.67 SF4.46: 10 residues within 4Å: Chain H: C.9, F.11, C.12, L.15, C.16, A.34, C.35, G.38, P.158, R.159 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.9, H:C.12, H:C.16, H:C.35 SF4.55: 13 residues within 4Å: Chain K: L.264, C.281, P.282, C.283, V.285, L.286, C.308, I.309, Y.310, C.311, G.312, A.313, C.314 4 PLIP interactions: 4 interactions with chain K, Metal complexes: K:C.281, K:C.308, K:C.311, K:C.314 SF4.56: 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 SF4.57: 12 residues within 4Å: Chain K: C.125, P.126, I.130, I.234, C.239, V.240, N.241, C.242, G.243, W.244, 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 SF4.58: 11 residues within 4Å: Chain K: I.110, C.115, I.116, Q.117, C.118, K.119, C.121, I.132, 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 SF4.59: 11 residues within 4Å: Chain K: C.154, I.155, Y.156, C.157, G.158, C.160, I.187, C.204, P.205, V.206, I.209 4 PLIP interactions: 4 interactions with chain K, Metal complexes: K:C.154, K:C.157, K:C.160, K:C.204 SF4.60: 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 SF4.61: 9 residues within 4Å: Chain K: C.41, V.43, I.46, C.71, V.72, 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 SF4.62: 11 residues within 4Å: Chain K: F.26, 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 SF4.68: 12 residues within 4Å: Chain L: C.12, H.13, G.14, C.15, G.16, N.17, C.18, V.53, 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 SF4.69: 14 residues within 4Å: Chain K: P.319 Chain L: L.5, C.22, P.23, V.24, I.45, M.46, C.61, G.62, K.63, C.64, G.65, T.66, 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.12: 5 residues within 4Å: Chain B: C.118 Chain D: R.9 Ligands: MGD.13, MGD.14, H2S.15 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.118 W.47: 5 residues within 4Å: Chain H: C.118 Chain J: R.9 Ligands: MGD.48, MGD.49, H2S.50 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.13: 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, I.384, V.385, D.414 Chain D: T.7, G.8, R.9, I.17, K.21, M.80, A.84, N.85, F.100, K.101 Ligands: W.12, MGD.14, H2S.15 23 PLIP interactions: 9 interactions with chain D, 14 interactions with chain B Hydrogen bonds: D:T.7, D:R.9, D:R.9, D:K.21, D:N.85, D:N.85, B:K.41, B:H.258, B:A.342, B:D.344, B:H.348, B:I.365, B:V.385 Water bridges: D:K.21, D:K.21, B:Y.291, B:Y.291 Salt bridges: D:K.21, B:H.290, B:H.290, B:H.348, B:H.348, B:D.414 MGD.14: 38 residues within 4Å: Chain B: F.11, I.37, C.118, 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, Y.77, M.80, K.101, N.102 Ligands: W.12, MGD.13, H2S.15 24 PLIP interactions: 11 interactions with chain D, 13 interactions with chain B Hydrogen bonds: D:N.6, D:R.9, D:R.9, D:Q.13, D:G.14, D:Y.77, 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:D.206 Salt bridges: D:R.9, D:R.9, D:K.101, B:D.185, B:D.206 MGD.48: 37 residues within 4Å: Chain H: F.11, I.37, C.118, W.149, G.150, C.151, N.152, H.155, A.156, H.157, V.184, D.185, P.186, R.187, T.189, 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.47, MGD.49, H2S.50 25 PLIP interactions: 15 interactions with chain H, 10 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:M.254, H:S.259, J:N.6, J:R.9, J:R.9, J:Q.13, J:G.14, J:N.102 Water bridges: H:N.152, H:H.157, 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 MGD.49: 35 residues within 4Å: Chain H: K.41, C.91, T.114, V.117, C.118, M.254, H.258, H.290, I.341, A.342, S.343, D.344, H.348, I.365, E.366, P.367, H.368, T.370, P.382, I.384, V.385, D.414 Chain J: T.7, G.8, R.9, I.17, K.21, M.80, A.84, N.85, F.100, K.101 Ligands: W.47, MGD.48, H2S.50 25 PLIP interactions: 15 interactions with chain H, 10 interactions with chain J Hydrogen bonds: H:K.41, H:A.342, H:D.344, H:H.348, H:I.365, H:V.385, J:T.7, J:R.9, J:R.9, J:K.21, J:N.85, J:N.85 Water bridges: H:Y.87, H:Y.87, H:H.368, H:T.370, J:I.17, J:K.21, J:K.21 Salt bridges: H:H.290, H:H.290, H:H.348, H:H.348, H:D.414, J:K.21

2 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.15: 8 residues within 4Å: Chain B: T.114, C.118, G.289, H.290, V.293 Ligands: W.12, MGD.13, MGD.14 No protein-ligand interaction detected (PLIP) H2S.50: 8 residues within 4Å: Chain H: T.114, C.118, G.289, H.290, V.293 Ligands: W.47, MGD.48, MGD.49 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.18: 7 residues within 4Å: Chain B: D.128 Chain C: S.139, Y.140, G.142, D.143, E.164, Y.165 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:S.139, C:Y.140, C:D.143, B:D.128, H2O.24 CA.53: 7 residues within 4Å: Chain H: D.128 Chain I: S.139, Y.140, G.142, D.143, E.164, Y.165 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain H Metal complexes: I:S.139, I:Y.140, I:D.143, H:D.128

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 B: 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
I

B
B

H
J

C
C

I
K

D
D

J
L

E
F

K
N

F
G

L
P

Tungsten formylmethanofuran dehydrogenase subunit fwdA

Tungsten formylmethanofuran dehydrogenase subunit B

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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