SMTL ID : 1kqg.1

FORMATE DEHYDROGENASE N FROM E. COLI

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-oligomer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: C.50, Y.52, C.53, V.55, G.56, C.57, L.91, C.92, K.94, G.95, P.238, V.239 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.50, A:C.53, A:C.57, A:C.92 SF4.2: 12 residues within 4Å: Chain B: C.39, I.40, G.41, C.42, K.43, A.44, C.45, M.80, C.179, P.180, T.181, I.184 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.39, B:C.42, B:C.45, B:C.179 SF4.3: 11 residues within 4Å: Chain B: K.32, C.49, N.53, T.78, K.97, C.160, T.161, L.162, C.163, P.173, C.175 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.49, B:C.160, B:C.163, B:C.175 SF4.4: 14 residues within 4Å: Chain B: C.100, M.101, H.102, C.103, P.106, G.107, C.108, V.126, C.143, P.144, F.145, I.147, P.148, K.159 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.100, B:C.103, B:C.108, B:C.143 SF4.5: 13 residues within 4Å: Chain B: C.112, P.113, S.114, A.117, I.118, C.133, I.134, G.135, C.136, G.137, Y.138, C.139, V.157 5 PLIP interactions: 5 interactions with chain B, pi-Cation interactions: B:F.128 Metal complexes: B:C.112, B:C.133, B:C.136, B:C.139 SF4.13: 12 residues within 4Å: Chain D: C.50, Y.52, C.53, V.55, G.56, C.57, L.91, C.92, K.94, G.95, P.238, V.239 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.50, D:C.53, D:C.57, D:C.92 SF4.14: 12 residues within 4Å: Chain E: C.39, I.40, G.41, C.42, K.43, A.44, C.45, M.80, C.179, P.180, T.181, I.184 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.39, E:C.42, E:C.45, E:C.179 SF4.15: 11 residues within 4Å: Chain E: K.32, C.49, N.53, T.78, K.97, C.160, T.161, L.162, C.163, P.173, C.175 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.49, E:C.160, E:C.163, E:C.175 SF4.16: 14 residues within 4Å: Chain E: C.100, M.101, H.102, C.103, P.106, G.107, C.108, V.126, C.143, P.144, F.145, I.147, P.148, K.159 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.100, E:C.103, E:C.108, E:C.143 SF4.17: 13 residues within 4Å: Chain E: C.112, P.113, S.114, A.117, I.118, C.133, I.134, G.135, C.136, G.137, Y.138, C.139, V.157 5 PLIP interactions: 5 interactions with chain E, pi-Cation interactions: E:F.128 Metal complexes: E:C.112, E:C.133, E:C.136, E:C.139 SF4.25: 12 residues within 4Å: Chain G: C.50, Y.52, C.53, V.55, G.56, C.57, L.91, C.92, K.94, G.95, P.238, V.239 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.50, G:C.53, G:C.57, G:C.92 SF4.26: 12 residues within 4Å: Chain H: C.39, I.40, G.41, C.42, K.43, A.44, C.45, M.80, C.179, P.180, T.181, I.184 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.39, H:C.42, H:C.45, H:C.179 SF4.27: 11 residues within 4Å: Chain H: K.32, C.49, N.53, T.78, K.97, C.160, T.161, L.162, C.163, P.173, C.175 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.49, H:C.160, H:C.163, H:C.175 SF4.28: 14 residues within 4Å: Chain H: C.100, M.101, H.102, C.103, P.106, G.107, C.108, V.126, C.143, P.144, F.145, I.147, P.148, K.159 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.100, H:C.103, H:C.108, H:C.143 SF4.29: 13 residues within 4Å: Chain H: C.112, P.113, S.114, A.117, I.118, C.133, I.134, G.135, C.136, G.137, Y.138, C.139, V.157 5 PLIP interactions: 5 interactions with chain H, pi-Cation interactions: H:F.128 Metal complexes: H:C.112, H:C.133, H:C.136, H:C.139

6 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.6: 35 residues within 4Å: Chain A: Y.101, G.168, A.169, Q.192, V.195, U.196, L.410, Q.414, H.448, Q.555, G.556, F.557, N.558, S.562, I.582, D.583, P.584, L.585, T.587, S.616, T.617, D.649, T.894, R.896, F.901, H.902, T.903, W.904, I.974, N.989, T.992, Y.1005, K.1006 Ligands: MGD.7, 6MO.8 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:Y.101, A:G.168, A:Q.192, A:Q.414, A:N.558, A:N.558, A:S.562, A:S.562, A:I.582, A:I.582, A:S.616, A:T.894, A:T.894, A:R.896, A:R.896, A:T.903, A:N.989 Water bridges: A:T.51, A:S.170, A:T.617 Salt bridges: A:H.448, A:H.448, A:D.583, A:D.649, A:H.902, A:H.902 pi-Cation interactions: A:Y.1005 MGD.7: 37 residues within 4Å: Chain A: C.53, K.94, U.196, G.230, G.231, N.232, E.235, A.236, H.237, V.258, D.259, P.260, R.261, T.263, I.275, S.277, G.278, D.280, A.409, L.410, G.411, W.412, H.415, G.447, H.448, T.893, Y.895, R.896, L.897, T.898, H.900, F.901, H.902, H.975, K.1006 Ligands: MGD.6, 6MO.8 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:K.94, A:G.230, A:N.232, A:N.232, A:A.236, A:V.258, A:R.261, A:R.261, A:G.278, A:L.410, A:G.411, A:T.893, A:R.896, A:R.896, A:L.897, A:H.902 Water bridges: A:G.231, A:G.231, A:D.280 Salt bridges: A:D.280, A:R.896, A:K.1006 MGD.18: 35 residues within 4Å: Chain D: Y.101, G.168, A.169, Q.192, V.195, U.196, L.410, Q.414, H.448, Q.555, G.556, F.557, N.558, S.562, I.582, D.583, P.584, L.585, T.587, S.616, T.617, D.649, T.894, R.896, F.901, H.902, T.903, W.904, I.974, N.989, T.992, Y.1005, K.1006 Ligands: MGD.19, 6MO.20 27 PLIP interactions: 27 interactions with chain D Hydrogen bonds: D:Y.101, D:G.168, D:Q.192, D:Q.414, D:N.558, D:N.558, D:S.562, D:S.562, D:I.582, D:I.582, D:S.616, D:T.894, D:T.894, D:R.896, D:R.896, D:T.903, D:T.903, D:N.989 Water bridges: D:T.51, D:S.170 Salt bridges: D:H.448, D:H.448, D:D.583, D:D.649, D:H.902, D:H.902 pi-Cation interactions: D:Y.1005 MGD.19: 37 residues within 4Å: Chain D: C.53, K.94, U.196, G.230, G.231, N.232, E.235, A.236, H.237, V.258, D.259, P.260, R.261, T.263, I.275, S.277, G.278, D.280, A.409, L.410, G.411, W.412, H.415, G.447, H.448, T.893, Y.895, R.896, L.897, T.898, H.900, F.901, H.902, H.975, K.1006 Ligands: MGD.18, 6MO.20 23 PLIP interactions: 23 interactions with chain D Hydrogen bonds: D:K.94, D:G.230, D:N.232, D:N.232, D:A.236, D:V.258, D:R.261, D:R.261, D:G.278, D:L.410, D:G.411, D:T.893, D:R.896, D:R.896, D:L.897, D:H.902 Water bridges: D:G.231, D:G.231, D:H.237, D:D.280 Salt bridges: D:D.280, D:R.896, D:K.1006 MGD.30: 35 residues within 4Å: Chain G: Y.101, G.168, A.169, Q.192, V.195, U.196, L.410, Q.414, H.448, Q.555, G.556, F.557, N.558, S.562, I.582, D.583, P.584, L.585, T.587, S.616, T.617, D.649, T.894, R.896, F.901, H.902, T.903, W.904, I.974, N.989, T.992, Y.1005, K.1006 Ligands: MGD.31, 6MO.32 28 PLIP interactions: 28 interactions with chain G Hydrogen bonds: G:G.168, G:Q.192, G:Q.414, G:N.558, G:N.558, G:S.562, G:S.562, G:I.582, G:I.582, G:S.616, G:T.894, G:T.894, G:R.896, G:R.896, G:T.903, G:N.989 Water bridges: G:T.51, G:S.170, G:T.617, G:D.649, G:D.649 Salt bridges: G:H.448, G:H.448, G:D.583, G:D.649, G:H.902, G:H.902 pi-Cation interactions: G:Y.1005 MGD.31: 37 residues within 4Å: Chain G: C.53, K.94, U.196, G.230, G.231, N.232, E.235, A.236, H.237, V.258, D.259, P.260, R.261, T.263, I.275, S.277, G.278, D.280, A.409, L.410, G.411, W.412, H.415, G.447, H.448, T.893, Y.895, R.896, L.897, T.898, H.900, F.901, H.902, H.975, K.1006 Ligands: MGD.30, 6MO.32 21 PLIP interactions: 21 interactions with chain G Hydrogen bonds: G:K.94, G:G.230, G:N.232, G:N.232, G:A.236, G:V.258, G:R.261, G:R.261, G:G.278, G:L.410, G:G.411, G:R.896, G:R.896, G:L.897, G:H.902 Water bridges: G:G.231, G:G.231, G:D.280 Salt bridges: G:D.280, G:R.896, G:K.1006

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

6MO.8: 4 residues within 4Å: Chain A: U.196, G.447 Ligands: MGD.6, MGD.7 No protein-ligand interaction detected (PLIP) 6MO.20: 4 residues within 4Å: Chain D: U.196, G.447 Ligands: MGD.18, MGD.19 No protein-ligand interaction detected (PLIP) 6MO.32: 4 residues within 4Å: Chain G: U.196, G.447 Ligands: MGD.30, MGD.31 No protein-ligand interaction detected (PLIP)

6 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.9: 26 residues within 4Å: Chain B: Y.138, W.253, K.258 Chain C: F.25, V.28, A.29, G.32, F.35, F.36, R.54, H.57, P.58, G.61, I.62, I.124, L.127, L.128, G.131, V.132, I.134, W.135, H.155, A.156, G.159, L.162, I.163 24 PLIP interactions: 18 interactions with chain C, 6 interactions with chain B, Hydrophobic interactions: C:F.25, C:V.28, C:A.29, C:F.35, C:F.35, C:P.58, C:I.124, C:L.127, C:L.128, C:I.134, C:I.134, C:W.135, C:A.156, C:L.162, C:I.163, B:Y.138 Hydrogen bonds: C:G.53, B:Y.138, B:Y.138 Metal complexes: C:H.57, C:H.155 Water bridges: B:K.258 Salt bridges: B:K.254, B:K.258 HEM.10: 19 residues within 4Å: Chain C: R.9, H.18, W.19, V.21, V.22, F.25, L.68, F.75, N.79, Y.109, Q.113, F.117, I.166, H.169, M.170, A.173, S.179, M.183 Ligands: HQO.11 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:W.19, C:V.21, C:V.22, C:V.22, C:F.25, C:L.68, C:F.75, C:I.166, C:M.183 Hydrogen bonds: C:N.79, C:Q.113, C:Q.113 Salt bridges: C:R.9 pi-Stacking: C:W.19 Metal complexes: C:H.18, C:H.169 HEM.21: 26 residues within 4Å: Chain E: Y.138, W.253, K.258 Chain F: F.25, V.28, A.29, G.32, F.35, F.36, R.54, H.57, P.58, G.61, I.62, I.124, L.127, L.128, G.131, V.132, I.134, W.135, H.155, A.156, G.159, L.162, I.163 24 PLIP interactions: 18 interactions with chain F, 6 interactions with chain E, Hydrophobic interactions: F:F.25, F:V.28, F:A.29, F:F.35, F:F.35, F:P.58, F:I.124, F:L.127, F:L.128, F:I.134, F:I.134, F:W.135, F:A.156, F:L.162, F:I.163, E:Y.138 Hydrogen bonds: F:G.53, E:Y.138, E:Y.138 Metal complexes: F:H.57, F:H.155 Water bridges: E:K.258 Salt bridges: E:K.254, E:K.258 HEM.22: 19 residues within 4Å: Chain F: R.9, H.18, W.19, V.21, V.22, F.25, L.68, F.75, N.79, Y.109, Q.113, F.117, I.166, H.169, M.170, A.173, S.179, M.183 Ligands: HQO.23 16 PLIP interactions: 16 interactions with chain F, Hydrophobic interactions: F:W.19, F:V.21, F:V.22, F:V.22, F:F.25, F:L.68, F:F.75, F:I.166, F:M.183 Hydrogen bonds: F:N.79, F:Q.113, F:Q.113 Salt bridges: F:R.9 pi-Stacking: F:W.19 Metal complexes: F:H.18, F:H.169 HEM.33: 26 residues within 4Å: Chain H: Y.138, W.253, K.258 Chain I: F.25, V.28, A.29, G.32, F.35, F.36, R.54, H.57, P.58, G.61, I.62, I.124, L.127, L.128, G.131, V.132, I.134, W.135, H.155, A.156, G.159, L.162, I.163 23 PLIP interactions: 18 interactions with chain I, 5 interactions with chain H, Hydrophobic interactions: I:F.25, I:V.28, I:A.29, I:F.35, I:F.35, I:P.58, I:I.124, I:L.127, I:L.128, I:I.134, I:I.134, I:W.135, I:A.156, I:L.162, I:I.163, H:Y.138 Hydrogen bonds: I:G.53, H:Y.138 Metal complexes: I:H.57, I:H.155 Water bridges: H:K.258 Salt bridges: H:K.254, H:K.258 HEM.34: 19 residues within 4Å: Chain I: R.9, H.18, W.19, V.21, V.22, F.25, L.68, F.75, N.79, Y.109, Q.113, F.117, I.166, H.169, M.170, A.173, S.179, M.183 Ligands: HQO.35 16 PLIP interactions: 16 interactions with chain I, Hydrophobic interactions: I:W.19, I:V.21, I:V.22, I:V.22, I:F.25, I:L.68, I:F.75, I:I.166, I:M.183 Hydrogen bonds: I:N.79, I:Q.113, I:Q.113 Salt bridges: I:R.9 pi-Stacking: I:W.19 Metal complexes: I:H.18, I:H.169

3 x HQO: 2-HEPTYL-4-HYDROXY QUINOLINE N-OXIDE(Non-covalent)

HQO.11: 9 residues within 4Å: Chain C: N.110, G.112, Q.113, M.116, H.169, M.172, A.173, V.176 Ligands: HEM.10 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:A.173 Hydrogen bonds: C:N.110 Water bridges: C:E.100, C:E.100 HQO.23: 9 residues within 4Å: Chain F: N.110, G.112, Q.113, M.116, H.169, M.172, A.173, V.176 Ligands: HEM.22 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:A.173 Hydrogen bonds: F:N.110 Water bridges: F:E.100, F:E.100 HQO.35: 9 residues within 4Å: Chain I: N.110, G.112, Q.113, M.116, H.169, M.172, A.173, V.176 Ligands: HEM.34 4 PLIP interactions: 4 interactions with chain I Hydrophobic interactions: I:A.173 Hydrogen bonds: I:N.110 Water bridges: I:E.100, I:E.100

3 x CDL: CARDIOLIPIN(Non-covalent)

CDL.12: 18 residues within 4Å: Chain B: N.15, S.16, I.17, P.259, A.262, A.263, F.265, I.266 Chain C: F.25, F.26, F.37, P.38, T.39, L.40 Chain I: F.26, L.27, F.47, M.52 17 PLIP interactions: 9 interactions with chain B, 6 interactions with chain C, 2 interactions with chain I Hydrophobic interactions: B:I.17, B:A.262, B:A.263, B:F.265, B:I.266, B:I.266, C:F.25, C:F.26, C:F.37, I:F.26, I:L.27 Hydrogen bonds: B:N.15, B:S.16, B:S.16, C:T.39, C:T.39 Water bridges: C:T.39 CDL.24: 18 residues within 4Å: Chain C: F.26, L.27, F.47, M.52 Chain E: N.15, S.16, I.17, P.259, A.262, A.263, F.265, I.266 Chain F: F.25, F.26, F.37, P.38, T.39, L.40 17 PLIP interactions: 9 interactions with chain E, 6 interactions with chain F, 2 interactions with chain C Hydrophobic interactions: E:I.17, E:A.262, E:A.263, E:F.265, E:I.266, E:I.266, F:F.25, F:F.26, F:F.37, C:F.26, C:L.27 Hydrogen bonds: E:N.15, E:S.16, E:S.16, F:T.39, F:T.39 Water bridges: F:T.39 CDL.36: 18 residues within 4Å: Chain F: F.26, L.27, F.47, M.52 Chain H: N.15, S.16, I.17, P.259, A.262, A.263, F.265, I.266 Chain I: F.25, F.26, F.37, P.38, T.39, L.40 17 PLIP interactions: 9 interactions with chain H, 6 interactions with chain I, 2 interactions with chain F Hydrophobic interactions: H:I.17, H:A.262, H:A.263, H:F.265, H:I.266, H:I.266, I:F.25, I:F.26, I:F.37, F:F.26, F:L.27 Hydrogen bonds: H:N.15, H:S.16, H:S.16, I:T.39, I:T.39 Water bridges: I:T.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jormakka, M. et al., Molecular basis of proton motive force generation: structure of formate dehydrogenase-N. Science (2002)

Release Date

2002-03-15

Peptides

FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, MAJOR SUBUNIT: ADG
FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, IRON-SULFUR SUBUNIT: BEH
FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, CYTOCHROME B556(FDN) SUBUNIT: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

B
B

E
B

H
B

C
C

F
C

I
C

Membrane

We predict this structure to be a membrane protein.
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FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, MAJOR SUBUNIT

FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, IRON-SULFUR SUBUNIT

FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, CYTOCHROME B556(FDN) SUBUNIT

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