- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- hetero-2-2-2-2-mer
- Ligands
- 2 x SE: SELENIUM ATOM(Non-covalent)
- 3 x NO3: NITRATE ION(Non-functional Binders)
NO3.2: 9 residues within 4Å:- Chain A: R.278, H.279, V.316, G.348, A.349, F.350, F.353, G.354, Q.357
8 PLIP interactions:8 interactions with chain A- Hydrogen bonds: A:R.278, A:H.279, A:G.348, A:F.350, A:F.350, A:F.353, A:G.354, A:Q.357
NO3.9: 6 residues within 4Å:- Chain C: C.222, R.265, P.266, S.267, V.268, K.271
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:C.222, C:R.265, C:S.267, C:S.267
NO3.14: 9 residues within 4Å:- Chain E: R.278, H.279, V.316, G.348, A.349, F.350, F.353, G.354, Q.357
8 PLIP interactions:8 interactions with chain E- Hydrogen bonds: E:R.278, E:H.279, E:H.279, E:F.350, E:F.350, E:F.353, E:G.354, E:Q.357
- 2 x MG: MAGNESIUM ION(Non-covalent)
MG.3: 7 residues within 4Å:- Chain A: T.207, N.209, D.213, K.242, L.243, D.244, Q.248
5 PLIP interactions:4 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:T.207, A:D.213, A:K.242, A:L.243, H2O.1
MG.4: 6 residues within 4Å:- Chain A: H.279, T.306, Y.309, A.310, S.311, S.347
5 PLIP interactions:5 interactions with chain A- Metal complexes: A:T.306, A:T.306, A:Y.309, A:A.310, A:S.347
- 2 x MOS: DIOXOTHIOMOLYBDENUM(VI) ION(Non-covalent)
MOS.5: 10 residues within 4Å:- Chain A: Q.208, G.240, L.243, F.353
- Chain B: T.84, S.85, A.86, E.289
- Ligands: SE.1, MCN.6
2 PLIP interactions:1 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:A.86, A:Q.208
MOS.16: 9 residues within 4Å:- Chain E: Q.208, G.240, L.243
- Chain F: T.84, S.85, A.86, E.289
- Ligands: SE.12, MCN.17
2 PLIP interactions:1 interactions with chain F, 1 interactions with chain E- Hydrogen bonds: F:A.86, E:Q.208
- 2 x MCN: PTERIN CYTOSINE DINUCLEOTIDE(Non-covalent)
MCN.6: 35 residues within 4Å:- Chain A: G.237, G.238, F.239, G.240, R.351
- Chain B: I.45, G.46, Q.47, G.48, S.49, T.84, S.85, A.86, S.87, R.88, Q.89, T.90, V.211, T.213, P.214, I.215, N.216, M.219, V.220, Q.223, A.284, K.285, G.286, V.287, G.288, E.289
- Chain D: Q.100, C.138
- Ligands: SE.1, MOS.5
20 PLIP interactions:16 interactions with chain B, 1 interactions with chain D, 3 interactions with chain A- Hydrophobic interactions: B:V.287
- Hydrogen bonds: B:Q.47, B:G.48, B:R.88, B:Q.89, B:T.90, B:T.90, B:T.213, B:I.215, B:N.216, B:Q.223, B:K.285, B:V.287, B:G.288, D:Q.100, A:G.238, A:F.239
- Water bridges: B:T.90, B:L.91, A:R.351
MCN.17: 35 residues within 4Å:- Chain E: G.237, G.238, F.239, G.240, R.351
- Chain F: I.45, G.46, Q.47, G.48, S.49, T.84, S.85, A.86, S.87, R.88, Q.89, T.90, V.211, T.213, P.214, I.215, N.216, M.219, V.220, Q.223, A.284, K.285, G.286, V.287, G.288, E.289
- Chain H: Q.100, C.138
- Ligands: SE.12, MOS.16
18 PLIP interactions:15 interactions with chain F, 1 interactions with chain H, 2 interactions with chain E- Hydrophobic interactions: F:V.287
- Hydrogen bonds: F:Q.47, F:G.48, F:R.88, F:Q.89, F:T.90, F:I.215, F:N.216, F:Q.223, F:K.285, F:K.285, F:V.287, F:G.288, H:Q.100, E:G.238, E:F.239
- Water bridges: F:T.90, F:L.91
- 2 x NIO: NICOTINIC ACID(Non-covalent)
NIO.7: 9 residues within 4Å:- Chain A: I.83, Y.312, A.315, R.319, F.353
- Chain B: N.17, T.18, L.20, A.86
6 PLIP interactions:4 interactions with chain B, 2 interactions with chain A- Hydrophobic interactions: B:N.17, B:A.86, A:A.315, A:F.353
- Hydrogen bonds: B:T.18, B:T.18
NIO.13: 6 residues within 4Å:- Chain A: E.198
- Chain E: V.15, E.19
- Chain F: V.70, T.71, W.72
6 PLIP interactions:5 interactions with chain F, 1 interactions with chain A- Hydrogen bonds: F:V.70, F:W.72
- Water bridges: F:V.70
- Salt bridges: F:H.69
- pi-Stacking: F:W.72
- Hydrophobic interactions: A:E.198
- 2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)
FAD.8: 33 residues within 4Å:- Chain C: I.29, I.30, A.31, G.32, G.33, T.34, D.35, L.36, I.38, A.73, F.77, Q.99, V.100, G.101, I.105, G.109, T.110, G.113, N.114, S.116, T.117, G.122, D.123, R.160, L.163, I.168, M.169, K.187, A.195
- Chain D: E.44, G.45, E.46, C.63
29 PLIP interactions:28 interactions with chain C, 1 interactions with chain D- Hydrophobic interactions: C:I.38, C:I.105, C:I.105, D:E.46
- Hydrogen bonds: C:I.29, C:I.29, C:A.31, C:G.32, C:G.33, C:T.34, C:D.35, C:D.35, C:L.36, C:G.101, C:T.110, C:N.114, C:S.116, C:D.123, C:D.123, C:R.160, C:R.160, C:M.169, C:M.169, C:K.187
- Water bridges: C:E.39, C:E.39, C:T.110, C:K.158, C:K.158
FAD.18: 34 residues within 4Å:- Chain G: I.29, I.30, A.31, G.32, G.33, T.34, D.35, L.36, I.38, I.53, F.77, V.100, G.101, I.105, L.108, G.109, T.110, G.113, N.114, S.116, T.117, G.122, D.123, G.124, R.160, L.163, I.168, M.169, K.187, A.195
- Chain H: E.44, G.45, E.46, C.63
29 PLIP interactions:28 interactions with chain G, 1 interactions with chain H- Hydrophobic interactions: G:I.38, G:I.105, G:I.105, H:E.46
- Hydrogen bonds: G:I.29, G:I.29, G:A.31, G:G.32, G:G.33, G:G.33, G:T.34, G:T.34, G:T.34, G:D.35, G:L.36, G:G.101, G:T.110, G:N.114, G:S.116, G:T.117, G:D.123, G:D.123, G:D.123, G:G.124, G:R.160, G:R.160, G:M.169, G:M.169, G:K.187
- 4 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
FES.10: 9 residues within 4Å:- Chain A: I.186
- Chain D: Q.100, C.101, G.102, C.104, C.136, R.137, C.138, T.139
4 PLIP interactions:4 interactions with chain D,- Metal complexes: D:C.101, D:C.104, D:C.136, D:C.138
FES.11: 11 residues within 4Å:- Chain D: E.40, G.41, C.42, S.43, G.45, E.46, C.47, G.48, C.50, T.60, C.62
4 PLIP interactions:4 interactions with chain D,- Metal complexes: D:C.42, D:C.47, D:C.50, D:C.62
FES.19: 8 residues within 4Å:- Chain E: I.186
- Chain H: Q.100, C.101, G.102, C.104, C.136, R.137, C.138
4 PLIP interactions:4 interactions with chain H,- Metal complexes: H:C.101, H:C.104, H:C.136, H:C.138
FES.20: 11 residues within 4Å:- Chain H: E.40, G.41, C.42, S.43, G.45, E.46, C.47, G.48, C.50, T.60, C.62
4 PLIP interactions:4 interactions with chain H,- Metal complexes: H:C.42, H:C.47, H:C.50, H:C.62
- 1 x CA: CALCIUM ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Wagener, N. et al., The Mo-Se active site of nicotinate dehydrogenase. Proc.Natl.Acad.Sci.USA (2009)
- Release Date
- 2009-06-30
- Peptides
- Nicotinate dehydrogenase large molybdopterin subunit: AE
Nicotinate dehydrogenase medium molybdopterin subunit: BF
Nicotinate dehydrogenase FAD-subunit: CG
Nicotinate dehydrogenase small FeS subunit: DH - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AE
EB
BF
FC
CG
GD
DH
H
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- hetero-2-2-2-2-mer
- Ligands
- 2 x SE: SELENIUM ATOM(Non-covalent)
- 3 x NO3: NITRATE ION(Non-functional Binders)
- 2 x MG: MAGNESIUM ION(Non-covalent)
- 2 x MOS: DIOXOTHIOMOLYBDENUM(VI) ION(Non-covalent)
- 2 x MCN: PTERIN CYTOSINE DINUCLEOTIDE(Non-covalent)
- 2 x NIO: NICOTINIC ACID(Non-covalent)
- 2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)
- 4 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- 1 x CA: CALCIUM ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Wagener, N. et al., The Mo-Se active site of nicotinate dehydrogenase. Proc.Natl.Acad.Sci.USA (2009)
- Release Date
- 2009-06-30
- Peptides
- Nicotinate dehydrogenase large molybdopterin subunit: AE
Nicotinate dehydrogenase medium molybdopterin subunit: BF
Nicotinate dehydrogenase FAD-subunit: CG
Nicotinate dehydrogenase small FeS subunit: DH - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AE
EB
BF
FC
CG
GD
DH
H