- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.60 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 3 x 6MO: MOLYBDENUM(VI) ION(Non-covalent)
- 15 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
SF4.2: 11 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, V.239
4 PLIP interactions:4 interactions with chain A,- Metal complexes: A:C.50, A:C.53, A:C.57, A:C.92
SF4.5: 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
SF4.6: 12 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, A.174, C.175
4 PLIP interactions:4 interactions with chain B,- Metal complexes: B:C.49, B:C.160, B:C.163, B:C.175
SF4.7: 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
SF4.8: 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: 11 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, V.239
4 PLIP interactions:4 interactions with chain D,- Metal complexes: D:C.50, D:C.53, D:C.57, D:C.92
SF4.16: 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
SF4.17: 12 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, A.174, C.175
4 PLIP interactions:4 interactions with chain E,- Metal complexes: E:C.49, E:C.160, E:C.163, E:C.175
SF4.18: 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
SF4.19: 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
SF4.24: 11 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, V.239
4 PLIP interactions:4 interactions with chain G,- Metal complexes: G:C.50, G:C.53, G:C.57, G:C.92
SF4.27: 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
SF4.28: 12 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, A.174, C.175
4 PLIP interactions:4 interactions with chain H,- Metal complexes: H:C.49, H:C.160, H:C.163, H:C.175
SF4.29: 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
SF4.30: 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.3: 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: 6MO.1, MGD.4
28 PLIP interactions:28 interactions with chain A- Hydrogen bonds: A:Y.101, A:Q.192, A:Q.414, A:N.558, A:N.558, A:S.562, A:S.562, A:I.582, A:S.616, A:T.894, A:T.894, A:R.896, A:R.896, A:T.903, A:N.989, A:N.989
- Water bridges: A:S.170, A:N.558, A:T.617, A:T.617
- Salt bridges: A:H.448, A:H.448, A:D.583, A:D.649, A:H.902, A:H.902
- pi-Stacking: A:Y.1005
- pi-Cation interactions: A:Y.1005
MGD.4: 36 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, 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: 6MO.1, MGD.3
26 PLIP interactions:26 interactions with chain A- Hydrogen bonds: A:G.230, A:N.232, A:N.232, A:E.235, 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:H.900, A:H.902, A:H.902
- Water bridges: A:K.94, A:K.94, A:G.231, A:H.237, A:D.280
- Salt bridges: A:D.259, A:D.280, A:R.896, A:K.1006
MGD.14: 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: 6MO.12, MGD.15
28 PLIP interactions:28 interactions with chain D- Hydrogen bonds: D:Y.101, D:Q.192, D:Q.414, D:N.558, D:N.558, D:S.562, D:S.562, 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, D:N.989
- Water bridges: D:S.170, D:N.558, D:T.617
- Salt bridges: D:H.448, D:H.448, D:D.583, D:D.649, D:H.902, D:H.902
- pi-Stacking: D:Y.1005
- pi-Cation interactions: D:Y.1005
MGD.15: 36 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, 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: 6MO.12, MGD.14
25 PLIP interactions:25 interactions with chain D- Hydrogen bonds: D:G.230, D:N.232, D:N.232, D:E.235, 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:H.900, D:H.902, D:H.902
- Water bridges: D:K.94, D:K.94, D:G.231, D:D.280
- Salt bridges: D:D.259, D:D.280, D:R.896, D:K.1006
MGD.25: 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: 6MO.23, MGD.26
28 PLIP interactions:28 interactions with chain G- Hydrogen bonds: G:Q.192, G:Q.414, G:N.558, G:N.558, G:S.562, G:S.562, G:I.582, G:S.616, G:T.894, G:T.894, G:R.896, G:R.896, G:T.903, G:N.989, G:N.989
- Water bridges: G:S.170, G:N.558, 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-Stacking: G:Y.1005
- pi-Cation interactions: G:Y.1005
MGD.26: 36 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, 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: 6MO.23, MGD.25
25 PLIP interactions:25 interactions with chain G- Hydrogen bonds: G:G.230, G:N.232, G:N.232, G:E.235, 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:H.900, G:H.902, G:H.902
- Water bridges: G:K.94, G:K.94, G:G.231, G:H.237, G:D.280
- Salt bridges: G:D.259, G:D.280, G:R.896, G:K.1006
- 6 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
HEM.9: 25 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, 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: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
- pi-Stacking: C:H.57, C:H.155
- Metal complexes: C:H.57, C:H.155
- Hydrogen bonds: B:Y.138, B:Y.138
- 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, F.75, N.79, Y.109, Q.113, F.117, I.120, I.166, H.169, M.170, A.173, S.179, I.180, M.183
23 PLIP interactions:23 interactions with chain C,- Hydrophobic interactions: C:W.19, C:V.21, C:V.22, C:V.22, C:F.25, C:F.25, C:F.75, C:I.120, C:I.166, C:A.173, C:M.183
- Hydrogen bonds: C:N.79, C:Q.113, C:Q.113
- Salt bridges: C:R.9
- pi-Stacking: C:H.18, C:H.18, C:W.19, C:H.169, C:H.169, C:H.169
- Metal complexes: C:H.18, C:H.169
HEM.20: 25 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, 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: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
- pi-Stacking: F:H.57, F:H.155
- Metal complexes: F:H.57, F:H.155
- Hydrogen bonds: E:Y.138, E:Y.138
- Water bridges: E:K.258
- Salt bridges: E:K.254, E:K.258
HEM.21: 19 residues within 4Å:- Chain F: R.9, H.18, W.19, V.21, V.22, F.25, F.75, N.79, Y.109, Q.113, F.117, I.120, I.166, H.169, M.170, A.173, S.179, I.180, M.183
23 PLIP interactions:23 interactions with chain F,- Hydrophobic interactions: F:W.19, F:V.21, F:V.22, F:V.22, F:F.25, F:F.25, F:F.75, F:I.120, F:I.166, F:A.173, F:M.183
- Hydrogen bonds: F:N.79, F:Q.113, F:Q.113
- Salt bridges: F:R.9
- pi-Stacking: F:H.18, F:H.18, F:W.19, F:H.169, F:H.169, F:H.169
- Metal complexes: F:H.18, F:H.169
HEM.31: 25 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, I.134, W.135, H.155, A.156, G.159, L.162, I.163
23 PLIP interactions:5 interactions with chain H, 18 interactions with chain I,- Hydrophobic interactions: H:Y.138, I:F.25, I:V.28, I:A.29, I:F.35, I:F.35, 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
- Hydrogen bonds: H:Y.138
- Water bridges: H:K.258
- Salt bridges: H:K.254, H:K.258
- pi-Stacking: I:H.57, I:H.155
- Metal complexes: I:H.57, I:H.155
HEM.32: 19 residues within 4Å:- Chain I: R.9, H.18, W.19, V.21, V.22, F.25, F.75, N.79, Y.109, Q.113, F.117, I.120, I.166, H.169, M.170, A.173, S.179, I.180, M.183
23 PLIP interactions:23 interactions with chain I,- Hydrophobic interactions: I:W.19, I:V.21, I:V.22, I:V.22, I:F.25, I:F.25, I:F.75, I:I.120, I:I.166, I:A.173, I:M.183
- Hydrogen bonds: I:N.79, I:Q.113, I:Q.113
- Salt bridges: I:R.9
- pi-Stacking: I:H.18, I:H.18, I:W.19, I:H.169, I:H.169, I:H.169
- Metal complexes: I:H.18, I:H.169
- 3 x CDL: CARDIOLIPIN(Non-covalent)
CDL.11: 16 residues within 4Å:- Chain B: N.15, S.16, I.17, P.259, A.262, A.263, I.266
- Chain C: F.37, P.38, T.39, L.40, M.170
- Chain I: F.26, F.47, M.52, L.56
13 PLIP interactions:3 interactions with chain C, 8 interactions with chain B, 2 interactions with chain I- Hydrogen bonds: C:T.39, C:T.39, B:N.15, B:S.16, B:S.16
- Water bridges: C:T.39
- Hydrophobic interactions: B:I.17, B:A.262, B:A.263, B:I.266, B:I.266, I:F.26, I:L.56
CDL.22: 16 residues within 4Å:- Chain C: F.26, F.47, M.52, L.56
- Chain E: N.15, S.16, I.17, P.259, A.262, A.263, I.266
- Chain F: F.37, P.38, T.39, L.40, M.170
13 PLIP interactions:8 interactions with chain E, 2 interactions with chain C, 3 interactions with chain F- Hydrophobic interactions: E:I.17, E:A.262, E:A.263, E:I.266, E:I.266, C:F.26, C:L.56
- Hydrogen bonds: E:N.15, E:S.16, E:S.16, F:T.39, F:T.39
- Water bridges: F:T.39
CDL.33: 16 residues within 4Å:- Chain F: F.26, F.47, M.52, L.56
- Chain H: N.15, S.16, I.17, P.259, A.262, A.263, I.266
- Chain I: F.37, P.38, T.39, L.40, M.170
13 PLIP interactions:8 interactions with chain H, 3 interactions with chain I, 2 interactions with chain F- Hydrophobic interactions: H:I.17, H:A.262, H:A.263, H:I.266, H:I.266, F:F.26, F:L.56
- 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
AD
AG
AB
BE
BH
BC
CF
CI
C - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.60 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 3 x 6MO: MOLYBDENUM(VI) ION(Non-covalent)
- 15 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
- 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)
- 6 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
- 3 x CDL: CARDIOLIPIN(Non-covalent)
- 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
AD
AG
AB
BE
BH
BC
CF
CI
C - Membrane
-
We predict this structure to be a membrane protein.