- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.10 Å
- Oligo State
- homo-octamer
- Ligands
- 8 x ALA- ALA- TRP- LEU- PHE- GLU- ALA: peptide(Non-covalent)
- 8 x K: POTASSIUM ION(Non-covalent)
K.2: 7 residues within 4Å:- Chain A: N.64, D.126, I.128, F.129, V.158, V.160, S.162
5 PLIP interactions:5 interactions with chain A- Metal complexes: A:D.126, A:F.129, A:V.158, A:V.160, A:S.162
K.8: 7 residues within 4Å:- Chain B: N.64, D.126, I.128, F.129, V.158, V.160, S.162
5 PLIP interactions:5 interactions with chain B- Metal complexes: B:D.126, B:F.129, B:V.158, B:V.160, B:S.162
K.14: 7 residues within 4Å:- Chain C: N.64, D.126, I.128, F.129, V.158, V.160, S.162
5 PLIP interactions:5 interactions with chain C- Metal complexes: C:D.126, C:F.129, C:V.158, C:V.160, C:S.162
K.20: 7 residues within 4Å:- Chain D: N.64, D.126, I.128, F.129, V.158, V.160, S.162
5 PLIP interactions:5 interactions with chain D- Metal complexes: D:D.126, D:F.129, D:V.158, D:V.160, D:S.162
K.26: 7 residues within 4Å:- Chain E: N.64, D.126, I.128, F.129, V.158, V.160, S.162
5 PLIP interactions:5 interactions with chain E- Metal complexes: E:D.126, E:F.129, E:V.158, E:V.160, E:S.162
K.32: 7 residues within 4Å:- Chain F: N.64, D.126, I.128, F.129, V.158, V.160, S.162
5 PLIP interactions:5 interactions with chain F- Metal complexes: F:D.126, F:F.129, F:V.158, F:V.160, F:S.162
K.38: 7 residues within 4Å:- Chain G: N.64, D.126, I.128, F.129, V.158, V.160, S.162
5 PLIP interactions:5 interactions with chain G- Metal complexes: G:D.126, G:F.129, G:V.158, G:V.160, G:S.162
K.44: 7 residues within 4Å:- Chain H: N.64, D.126, I.128, F.129, V.158, V.160, S.162
5 PLIP interactions:5 interactions with chain H- Metal complexes: H:D.126, H:F.129, H:V.158, H:V.160, H:S.162
- 8 x MG: MAGNESIUM ION(Non-covalent)
MG.3: 2 residues within 4Å:- Chain A: K.414
- Ligands: ATP.5
No protein-ligand interaction detected (PLIP)MG.9: 2 residues within 4Å:- Chain B: K.414
- Ligands: ATP.11
No protein-ligand interaction detected (PLIP)MG.15: 2 residues within 4Å:- Chain C: K.414
- Ligands: ATP.17
No protein-ligand interaction detected (PLIP)MG.21: 2 residues within 4Å:- Chain D: K.414
- Ligands: ATP.23
No protein-ligand interaction detected (PLIP)MG.27: 2 residues within 4Å:- Chain E: K.414
- Ligands: ATP.29
No protein-ligand interaction detected (PLIP)MG.33: 2 residues within 4Å:- Chain F: K.414
- Ligands: ATP.35
No protein-ligand interaction detected (PLIP)MG.39: 2 residues within 4Å:- Chain G: K.414
- Ligands: ATP.41
No protein-ligand interaction detected (PLIP)MG.45: 2 residues within 4Å:- Chain H: K.414
- Ligands: ATP.47
No protein-ligand interaction detected (PLIP)- 16 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
ATP.4: 14 residues within 4Å:- Chain A: G.62, N.63, N.64, F.129, G.130, T.131, G.132, L.133, R.134, G.135, E.136, Y.141, D.159
- Ligands: GOL.6
15 PLIP interactions:15 interactions with chain A- Hydrogen bonds: A:N.63, A:N.64, A:G.130, A:T.131, A:T.131, A:T.131, A:G.132, A:L.133, A:R.134, A:E.136, A:D.159
- Water bridges: A:N.64, A:G.65, A:T.138
- Salt bridges: A:K.14
ATP.5: 22 residues within 4Å:- Chain A: H.378, K.414, S.415, A.416, T.418, G.432, N.433, T.434, L.436, S.437, K.438, G.439, G.440, S.441, G.442, D.443, L.445, H.470
- Chain D: R.237, S.239, K.241
- Ligands: MG.3
16 PLIP interactions:13 interactions with chain A, 3 interactions with chain D- Hydrogen bonds: A:S.415, A:T.418, A:T.418, A:S.437, A:G.440, A:G.442, A:D.443, A:D.443
- Water bridges: A:K.414, A:K.414, A:H.470
- Salt bridges: A:H.378, A:K.414, D:K.241, D:K.241, D:K.241
ATP.10: 14 residues within 4Å:- Chain B: G.62, N.63, N.64, F.129, G.130, T.131, G.132, L.133, R.134, G.135, E.136, Y.141, D.159
- Ligands: GOL.12
15 PLIP interactions:15 interactions with chain B- Hydrogen bonds: B:N.63, B:N.64, B:G.130, B:T.131, B:T.131, B:T.131, B:G.132, B:L.133, B:R.134, B:E.136, B:D.159
- Water bridges: B:N.64, B:G.65, B:T.138
- Salt bridges: B:K.14
ATP.11: 22 residues within 4Å:- Chain B: H.378, K.414, S.415, A.416, T.418, G.432, N.433, T.434, L.436, S.437, K.438, G.439, G.440, S.441, G.442, D.443, L.445, H.470
- Chain C: R.237, S.239, K.241
- Ligands: MG.9
16 PLIP interactions:13 interactions with chain B, 3 interactions with chain C- Hydrogen bonds: B:S.415, B:T.418, B:T.418, B:S.437, B:G.440, B:G.442, B:D.443, B:D.443
- Water bridges: B:K.414, B:K.414, B:H.470
- Salt bridges: B:H.378, B:K.414, C:K.241, C:K.241, C:K.241
ATP.16: 14 residues within 4Å:- Chain C: G.62, N.63, N.64, F.129, G.130, T.131, G.132, L.133, R.134, G.135, E.136, Y.141, D.159
- Ligands: GOL.18
15 PLIP interactions:15 interactions with chain C- Hydrogen bonds: C:N.63, C:N.64, C:G.130, C:T.131, C:T.131, C:T.131, C:G.132, C:L.133, C:R.134, C:E.136, C:D.159
- Water bridges: C:N.64, C:G.65, C:T.138
- Salt bridges: C:K.14
ATP.17: 22 residues within 4Å:- Chain A: R.237, S.239, K.241
- Chain C: H.378, K.414, S.415, A.416, T.418, G.432, N.433, T.434, L.436, S.437, K.438, G.439, G.440, S.441, G.442, D.443, L.445, H.470
- Ligands: MG.15
16 PLIP interactions:3 interactions with chain A, 13 interactions with chain C- Salt bridges: A:K.241, A:K.241, A:K.241, C:H.378, C:K.414
- Hydrogen bonds: C:S.415, C:T.418, C:T.418, C:S.437, C:G.440, C:G.442, C:D.443, C:D.443
- Water bridges: C:K.414, C:K.414, C:H.470
ATP.22: 14 residues within 4Å:- Chain D: G.62, N.63, N.64, F.129, G.130, T.131, G.132, L.133, R.134, G.135, E.136, Y.141, D.159
- Ligands: GOL.24
15 PLIP interactions:15 interactions with chain D- Hydrogen bonds: D:N.63, D:N.64, D:G.130, D:T.131, D:T.131, D:T.131, D:G.132, D:L.133, D:R.134, D:E.136, D:D.159
- Water bridges: D:N.64, D:G.65, D:T.138
- Salt bridges: D:K.14
ATP.23: 22 residues within 4Å:- Chain B: R.237, S.239, K.241
- Chain D: H.378, K.414, S.415, A.416, T.418, G.432, N.433, T.434, L.436, S.437, K.438, G.439, G.440, S.441, G.442, D.443, L.445, H.470
- Ligands: MG.21
16 PLIP interactions:13 interactions with chain D, 3 interactions with chain B- Hydrogen bonds: D:S.415, D:T.418, D:T.418, D:S.437, D:G.440, D:G.442, D:D.443, D:D.443
- Water bridges: D:K.414, D:K.414, D:H.470
- Salt bridges: D:H.378, D:K.414, B:K.241, B:K.241, B:K.241
ATP.28: 14 residues within 4Å:- Chain E: G.62, N.63, N.64, F.129, G.130, T.131, G.132, L.133, R.134, G.135, E.136, Y.141, D.159
- Ligands: GOL.30
13 PLIP interactions:13 interactions with chain E- Hydrogen bonds: E:N.63, E:N.64, E:G.130, E:T.131, E:T.131, E:G.132, E:L.133, E:R.134, E:E.136
- Water bridges: E:N.64, E:G.65, E:T.138
- Salt bridges: E:K.14
ATP.29: 22 residues within 4Å:- Chain E: H.378, K.414, S.415, A.416, T.418, G.432, N.433, T.434, L.436, S.437, K.438, G.439, G.440, S.441, G.442, D.443, L.445, H.470
- Chain H: R.237, S.239, K.241
- Ligands: MG.27
16 PLIP interactions:13 interactions with chain E, 3 interactions with chain H- Hydrogen bonds: E:S.415, E:T.418, E:S.437, E:G.440, E:G.442, E:D.443, E:D.443
- Water bridges: E:K.414, E:K.414, E:T.418, E:D.443
- Salt bridges: E:H.378, E:K.414, H:K.241, H:K.241, H:K.241
ATP.34: 14 residues within 4Å:- Chain F: G.62, N.63, N.64, F.129, G.130, T.131, G.132, L.133, R.134, G.135, E.136, Y.141, D.159
- Ligands: GOL.36
13 PLIP interactions:13 interactions with chain F- Hydrogen bonds: F:N.63, F:N.64, F:G.130, F:T.131, F:T.131, F:G.132, F:L.133, F:R.134, F:E.136
- Water bridges: F:N.64, F:G.65, F:T.138
- Salt bridges: F:K.14
ATP.35: 22 residues within 4Å:- Chain F: H.378, K.414, S.415, A.416, T.418, G.432, N.433, T.434, L.436, S.437, K.438, G.439, G.440, S.441, G.442, D.443, L.445, H.470
- Chain G: R.237, S.239, K.241
- Ligands: MG.33
16 PLIP interactions:13 interactions with chain F, 3 interactions with chain G- Hydrogen bonds: F:S.415, F:T.418, F:S.437, F:G.440, F:G.442, F:D.443, F:D.443
- Water bridges: F:K.414, F:K.414, F:T.418, F:D.443
- Salt bridges: F:H.378, F:K.414, G:K.241, G:K.241, G:K.241
ATP.40: 14 residues within 4Å:- Chain G: G.62, N.63, N.64, F.129, G.130, T.131, G.132, L.133, R.134, G.135, E.136, Y.141, D.159
- Ligands: GOL.42
13 PLIP interactions:13 interactions with chain G- Hydrogen bonds: G:N.63, G:N.64, G:G.130, G:T.131, G:T.131, G:G.132, G:L.133, G:R.134, G:E.136
- Water bridges: G:N.64, G:G.65, G:T.138
- Salt bridges: G:K.14
ATP.41: 22 residues within 4Å:- Chain E: R.237, S.239, K.241
- Chain G: H.378, K.414, S.415, A.416, T.418, G.432, N.433, T.434, L.436, S.437, K.438, G.439, G.440, S.441, G.442, D.443, L.445, H.470
- Ligands: MG.39
16 PLIP interactions:13 interactions with chain G, 3 interactions with chain E- Hydrogen bonds: G:S.415, G:T.418, G:S.437, G:G.440, G:G.442, G:D.443, G:D.443
- Water bridges: G:K.414, G:K.414, G:T.418, G:D.443
- Salt bridges: G:H.378, G:K.414, E:K.241, E:K.241, E:K.241
ATP.46: 14 residues within 4Å:- Chain H: G.62, N.63, N.64, F.129, G.130, T.131, G.132, L.133, R.134, G.135, E.136, Y.141, D.159
- Ligands: GOL.48
13 PLIP interactions:13 interactions with chain H- Hydrogen bonds: H:N.63, H:N.64, H:G.130, H:T.131, H:T.131, H:G.132, H:L.133, H:R.134, H:E.136
- Water bridges: H:N.64, H:G.65, H:T.138
- Salt bridges: H:K.14
ATP.47: 22 residues within 4Å:- Chain F: R.237, S.239, K.241
- Chain H: H.378, K.414, S.415, A.416, T.418, G.432, N.433, T.434, L.436, S.437, K.438, G.439, G.440, S.441, G.442, D.443, L.445, H.470
- Ligands: MG.45
16 PLIP interactions:13 interactions with chain H, 3 interactions with chain F- Hydrogen bonds: H:S.415, H:T.418, H:S.437, H:G.440, H:G.442, H:D.443, H:D.443
- Water bridges: H:K.414, H:K.414, H:T.418, H:D.443
- Salt bridges: H:H.378, H:K.414, F:K.241, F:K.241, F:K.241
- 8 x GOL: GLYCEROL(Non-functional Binders)
GOL.6: 7 residues within 4Å:- Chain A: D.17, L.31, M.32, D.67, F.184, I.208
- Ligands: ATP.4
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:D.17
- Water bridges: A:D.67, A:D.159
GOL.12: 7 residues within 4Å:- Chain B: D.17, L.31, M.32, D.67, F.184, I.208
- Ligands: ATP.10
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:D.17
- Water bridges: B:D.67, B:D.159
GOL.18: 7 residues within 4Å:- Chain C: D.17, L.31, M.32, D.67, F.184, I.208
- Ligands: ATP.16
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:D.17
- Water bridges: C:D.67, C:D.159
GOL.24: 7 residues within 4Å:- Chain D: D.17, L.31, M.32, D.67, F.184, I.208
- Ligands: ATP.22
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:D.17
- Water bridges: D:D.67, D:D.159
GOL.30: 7 residues within 4Å:- Chain E: D.17, L.31, M.32, D.67, F.184, I.208
- Ligands: ATP.28
3 PLIP interactions:3 interactions with chain E- Hydrogen bonds: E:D.17
- Water bridges: E:D.67, E:D.67
GOL.36: 7 residues within 4Å:- Chain F: D.17, L.31, M.32, D.67, F.184, I.208
- Ligands: ATP.34
3 PLIP interactions:3 interactions with chain F- Hydrogen bonds: F:D.17
- Water bridges: F:D.67, F:D.67
GOL.42: 7 residues within 4Å:- Chain G: D.17, L.31, M.32, D.67, F.184, I.208
- Ligands: ATP.40
3 PLIP interactions:3 interactions with chain G- Hydrogen bonds: G:D.17
- Water bridges: G:D.67, G:D.67
GOL.48: 7 residues within 4Å:- Chain H: D.17, L.31, M.32, D.67, F.184, I.208
- Ligands: ATP.46
3 PLIP interactions:3 interactions with chain H- Hydrogen bonds: H:D.17
- Water bridges: H:D.67, H:D.67
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Shumilin, I.A. et al., Identification of unknown protein function using metabolite cocktail screening. Structure (2012)
- Release Date
- 2011-07-27
- Peptides
- Bifunctional NAD(P)H-hydrate repair enzyme Nnr: ABCDEFGH
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
AE
AF
AG
AH
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.10 Å
- Oligo State
- homo-octamer
- Ligands
- 8 x ALA- ALA- TRP- LEU- PHE- GLU- ALA: peptide(Non-covalent)
- 8 x K: POTASSIUM ION(Non-covalent)
- 8 x MG: MAGNESIUM ION(Non-covalent)
- 16 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
- 8 x GOL: GLYCEROL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Shumilin, I.A. et al., Identification of unknown protein function using metabolite cocktail screening. Structure (2012)
- Release Date
- 2011-07-27
- Peptides
- Bifunctional NAD(P)H-hydrate repair enzyme Nnr: ABCDEFGH
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
AE
AF
AG
AH
A