- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.61 Å
- Oligo State
- homo-octamer
- Ligands
- 8 x ALA- TRP- LEU- PHE- GLU- ALA: Unknown peptide, probably from expression host(Non-covalent)
- 8 x K: POTASSIUM ION(Non-covalent)
K.2: 8 residues within 4Å:- Chain A: N.64, D.126, A.127, I.128, F.129, V.158, V.160, S.162
4 PLIP interactions:4 interactions with chain A- Metal complexes: A:D.126, A:F.129, A:V.160, A:S.162
K.8: 8 residues within 4Å:- Chain B: N.64, D.126, A.127, I.128, F.129, V.158, V.160, S.162
4 PLIP interactions:4 interactions with chain B- Metal complexes: B:D.126, B:F.129, B:V.160, B:S.162
K.14: 8 residues within 4Å:- Chain C: N.64, D.126, A.127, I.128, F.129, V.158, V.160, S.162
4 PLIP interactions:4 interactions with chain C- Metal complexes: C:D.126, C:F.129, C:V.160, C:S.162
K.20: 8 residues within 4Å:- Chain D: N.64, D.126, A.127, I.128, F.129, V.158, V.160, S.162
4 PLIP interactions:4 interactions with chain D- Metal complexes: D:D.126, D:F.129, D:V.160, D:S.162
K.26: 8 residues within 4Å:- Chain E: N.64, D.126, A.127, I.128, F.129, V.158, V.160, S.162
4 PLIP interactions:4 interactions with chain E- Metal complexes: E:D.126, E:F.129, E:V.160, E:S.162
K.32: 8 residues within 4Å:- Chain F: N.64, D.126, A.127, I.128, F.129, V.158, V.160, S.162
4 PLIP interactions:4 interactions with chain F- Metal complexes: F:D.126, F:F.129, F:V.160, F:S.162
K.38: 8 residues within 4Å:- Chain G: N.64, D.126, A.127, I.128, F.129, V.158, V.160, S.162
4 PLIP interactions:4 interactions with chain G- Metal complexes: G:D.126, G:F.129, G:V.160, G:S.162
K.44: 8 residues within 4Å:- Chain H: N.64, D.126, A.127, I.128, F.129, V.158, V.160, S.162
4 PLIP interactions:4 interactions with chain H- Metal complexes: H:D.126, H:F.129, H:V.160, H:S.162
- 8 x MG: MAGNESIUM ION(Non-functional Binders)
MG.3: 2 residues within 4Å:- Ligands: ATP.5, NPW.6
No protein-ligand interaction detected (PLIP)MG.9: 2 residues within 4Å:- Ligands: ATP.11, NPW.12
No protein-ligand interaction detected (PLIP)MG.15: 2 residues within 4Å:- Ligands: ATP.17, NPW.18
No protein-ligand interaction detected (PLIP)MG.21: 2 residues within 4Å:- Ligands: ATP.23, NPW.24
No protein-ligand interaction detected (PLIP)MG.27: 2 residues within 4Å:- Ligands: ATP.29, NPW.30
No protein-ligand interaction detected (PLIP)MG.33: 2 residues within 4Å:- Ligands: ATP.35, NPW.36
No protein-ligand interaction detected (PLIP)MG.39: 2 residues within 4Å:- Ligands: ATP.41, NPW.42
No protein-ligand interaction detected (PLIP)MG.45: 2 residues within 4Å:- Ligands: ATP.47, NPW.48
No protein-ligand interaction detected (PLIP)- 8 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)
NDP.4: 16 residues within 4Å:- Chain A: D.17, G.61, G.62, N.63, N.64, D.67, K.90, F.129, G.130, T.131, G.132, L.133, R.134, E.136, Y.141, D.159
15 PLIP interactions:15 interactions with chain A- Hydrogen bonds: A:N.63, A:N.64, A:N.64, A:G.130, A:T.131, A:T.131, A:G.132, A:R.134, A:E.136, A:D.159
- Water bridges: A:G.62, A:G.62, A:D.67
- Salt bridges: A:K.90
- pi-Stacking: A:Y.141
NDP.10: 16 residues within 4Å:- Chain B: D.17, G.61, G.62, N.63, N.64, D.67, K.90, F.129, G.130, T.131, G.132, L.133, R.134, E.136, Y.141, D.159
15 PLIP interactions:15 interactions with chain B- Hydrogen bonds: B:N.63, B:N.64, B:N.64, B:G.130, B:T.131, B:T.131, B:G.132, B:R.134, B:E.136, B:D.159
- Water bridges: B:G.62, B:G.62, B:D.67
- Salt bridges: B:K.90
- pi-Stacking: B:Y.141
NDP.16: 16 residues within 4Å:- Chain C: D.17, G.61, G.62, N.63, N.64, D.67, K.90, F.129, G.130, T.131, G.132, L.133, R.134, E.136, Y.141, D.159
15 PLIP interactions:15 interactions with chain C- Hydrogen bonds: C:N.63, C:N.64, C:N.64, C:G.130, C:T.131, C:T.131, C:G.132, C:R.134, C:E.136, C:D.159
- Water bridges: C:G.62, C:G.62, C:D.67
- Salt bridges: C:K.90
- pi-Stacking: C:Y.141
NDP.22: 16 residues within 4Å:- Chain D: D.17, G.61, G.62, N.63, N.64, D.67, K.90, F.129, G.130, T.131, G.132, L.133, R.134, E.136, Y.141, D.159
15 PLIP interactions:15 interactions with chain D- Hydrogen bonds: D:N.63, D:N.64, D:N.64, D:G.130, D:T.131, D:T.131, D:G.132, D:R.134, D:E.136, D:D.159
- Water bridges: D:G.62, D:G.62, D:D.67
- Salt bridges: D:K.90
- pi-Stacking: D:Y.141
NDP.28: 16 residues within 4Å:- Chain E: D.17, G.61, G.62, N.63, N.64, D.67, K.90, F.129, G.130, T.131, G.132, L.133, R.134, E.136, Y.141, D.159
17 PLIP interactions:17 interactions with chain E- Hydrogen bonds: E:N.63, E:N.64, E:N.64, E:D.67, E:G.130, E:T.131, E:T.131, E:G.132, E:R.134, E:E.136, E:D.159, E:D.159
- Water bridges: E:G.62, E:G.62, E:D.67
- Salt bridges: E:K.90
- pi-Stacking: E:Y.141
NDP.34: 16 residues within 4Å:- Chain F: D.17, G.61, G.62, N.63, N.64, D.67, K.90, F.129, G.130, T.131, G.132, L.133, R.134, E.136, Y.141, D.159
17 PLIP interactions:17 interactions with chain F- Hydrogen bonds: F:N.63, F:N.64, F:N.64, F:D.67, F:G.130, F:T.131, F:T.131, F:G.132, F:R.134, F:E.136, F:D.159, F:D.159
- Water bridges: F:G.62, F:G.62, F:D.67
- Salt bridges: F:K.90
- pi-Stacking: F:Y.141
NDP.40: 16 residues within 4Å:- Chain G: D.17, G.61, G.62, N.63, N.64, D.67, K.90, F.129, G.130, T.131, G.132, L.133, R.134, E.136, Y.141, D.159
17 PLIP interactions:17 interactions with chain G- Hydrogen bonds: G:N.63, G:N.64, G:N.64, G:D.67, G:G.130, G:T.131, G:T.131, G:G.132, G:R.134, G:E.136, G:D.159, G:D.159
- Water bridges: G:G.62, G:G.62, G:D.67
- Salt bridges: G:K.90
- pi-Stacking: G:Y.141
NDP.46: 16 residues within 4Å:- Chain H: D.17, G.61, G.62, N.63, N.64, D.67, K.90, F.129, G.130, T.131, G.132, L.133, R.134, E.136, Y.141, D.159
17 PLIP interactions:17 interactions with chain H- Hydrogen bonds: H:N.63, H:N.64, H:N.64, H:D.67, H:G.130, H:T.131, H:T.131, H:G.132, H:R.134, H:E.136, H:D.159, H:D.159
- Water bridges: H:G.62, H:G.62, H:D.67
- Salt bridges: H:K.90
- pi-Stacking: H:Y.141
- 8 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
ATP.5: 24 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, H.240, K.241
- Ligands: MG.3, NPW.6
14 PLIP interactions:10 interactions with chain A, 4 interactions with chain D- Hydrogen bonds: A:S.415, A:T.418, A:T.418, A:S.437, A:G.440, A:G.440, A:S.441, A:G.442, A:D.443, D:S.239, D:S.239
- Salt bridges: A:K.414, D:K.241, D:K.241
ATP.11: 24 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, H.240, K.241
- Ligands: MG.9, NPW.12
14 PLIP interactions:10 interactions with chain B, 4 interactions with chain C- Hydrogen bonds: B:S.415, B:T.418, B:T.418, B:S.437, B:G.440, B:G.440, B:S.441, B:G.442, B:D.443, C:S.239, C:S.239
- Salt bridges: B:K.414, C:K.241, C:K.241
ATP.17: 24 residues within 4Å:- Chain A: R.237, S.239, H.240, 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, NPW.18
14 PLIP interactions:10 interactions with chain C, 4 interactions with chain A- Hydrogen bonds: C:S.415, C:T.418, C:T.418, C:S.437, C:G.440, C:G.440, C:S.441, C:G.442, C:D.443, A:S.239, A:S.239
- Salt bridges: C:K.414, A:K.241, A:K.241
ATP.23: 24 residues within 4Å:- Chain B: R.237, S.239, H.240, 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, NPW.24
14 PLIP interactions:10 interactions with chain D, 4 interactions with chain B- Hydrogen bonds: D:S.415, D:T.418, D:T.418, D:S.437, D:G.440, D:G.440, D:S.441, D:G.442, D:D.443, B:S.239, B:S.239
- Salt bridges: D:K.414, B:K.241, B:K.241
ATP.29: 24 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, H.240, K.241
- Ligands: MG.27, NPW.30
14 PLIP interactions:10 interactions with chain E, 4 interactions with chain H- Hydrogen bonds: E:S.415, E:T.418, E:S.437, E:G.440, E:G.440, E:S.441, E:G.442, E:D.443, H:S.239, H:S.239
- Water bridges: E:D.443
- Salt bridges: E:K.414, H:K.241, H:K.241
ATP.35: 24 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, H.240, K.241
- Ligands: MG.33, NPW.36
14 PLIP interactions:10 interactions with chain F, 4 interactions with chain G- Hydrogen bonds: F:S.415, F:T.418, F:S.437, F:G.440, F:G.440, F:S.441, F:G.442, F:D.443, G:S.239, G:S.239
- Water bridges: F:D.443
- Salt bridges: F:K.414, G:K.241, G:K.241
ATP.41: 24 residues within 4Å:- Chain E: R.237, S.239, H.240, 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, NPW.42
14 PLIP interactions:10 interactions with chain G, 4 interactions with chain E- Hydrogen bonds: G:S.415, G:T.418, G:S.437, G:G.440, G:G.440, G:S.441, G:G.442, G:D.443, E:S.239, E:S.239
- Water bridges: G:D.443
- Salt bridges: G:K.414, E:K.241, E:K.241
ATP.47: 24 residues within 4Å:- Chain F: R.237, S.239, H.240, 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, NPW.48
14 PLIP interactions:10 interactions with chain H, 4 interactions with chain F- Hydrogen bonds: H:S.415, H:T.418, H:S.437, H:G.440, H:G.440, H:S.441, H:G.442, H:D.443, F:S.239, F:S.239
- Water bridges: H:D.443
- Salt bridges: H:K.414, F:K.241, F:K.241
- 8 x NPW: BETA-6-HYDROXY-1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE(Non-covalent)
NPW.6: 28 residues within 4Å:- Chain A: Y.256, G.258, A.259, G.327, P.328, G.329, L.330, A.355, D.356, N.359, H.378, P.379, G.380, E.381, R.384, G.439, G.440, D.443
- Chain D: H.240, K.241, G.242, K.246, P.292, E.293, L.294, I.295
- Ligands: MG.3, ATP.5
25 PLIP interactions:17 interactions with chain A, 8 interactions with chain D- Hydrogen bonds: A:G.258, A:A.259, A:G.327, A:G.329, A:L.330, A:D.356, A:N.359, A:N.359, A:H.378, A:G.380, A:G.440, A:D.443, A:D.443, D:K.241, D:P.292
- Salt bridges: A:H.378, A:H.378, A:R.384, D:K.241, D:K.246
- pi-Stacking: A:H.378, D:H.240, D:H.240
- Hydrophobic interactions: D:I.295
- Water bridges: D:K.241
NPW.12: 28 residues within 4Å:- Chain B: Y.256, G.258, A.259, G.327, P.328, G.329, L.330, A.355, D.356, N.359, H.378, P.379, G.380, E.381, R.384, G.439, G.440, D.443
- Chain C: H.240, K.241, G.242, K.246, P.292, E.293, L.294, I.295
- Ligands: MG.9, ATP.11
25 PLIP interactions:8 interactions with chain C, 17 interactions with chain B- Hydrophobic interactions: C:I.295
- Hydrogen bonds: C:K.241, C:P.292, B:G.258, B:A.259, B:G.327, B:G.329, B:L.330, B:D.356, B:N.359, B:N.359, B:H.378, B:G.380, B:G.440, B:D.443, B:D.443
- Water bridges: C:K.241
- Salt bridges: C:K.241, C:K.246, B:H.378, B:H.378, B:R.384
- pi-Stacking: C:H.240, C:H.240, B:H.378
NPW.18: 28 residues within 4Å:- Chain A: H.240, K.241, G.242, K.246, P.292, E.293, L.294, I.295
- Chain C: Y.256, G.258, A.259, G.327, P.328, G.329, L.330, A.355, D.356, N.359, H.378, P.379, G.380, E.381, R.384, G.439, G.440, D.443
- Ligands: MG.15, ATP.17
25 PLIP interactions:17 interactions with chain C, 8 interactions with chain A- Hydrogen bonds: C:G.258, C:A.259, C:G.327, C:G.329, C:L.330, C:D.356, C:N.359, C:N.359, C:H.378, C:G.380, C:G.440, C:D.443, C:D.443, A:K.241, A:P.292
- Salt bridges: C:H.378, C:H.378, C:R.384, A:K.241, A:K.246
- pi-Stacking: C:H.378, A:H.240, A:H.240
- Hydrophobic interactions: A:I.295
- Water bridges: A:K.241
NPW.24: 28 residues within 4Å:- Chain B: H.240, K.241, G.242, K.246, P.292, E.293, L.294, I.295
- Chain D: Y.256, G.258, A.259, G.327, P.328, G.329, L.330, A.355, D.356, N.359, H.378, P.379, G.380, E.381, R.384, G.439, G.440, D.443
- Ligands: MG.21, ATP.23
25 PLIP interactions:8 interactions with chain B, 17 interactions with chain D- Hydrophobic interactions: B:I.295
- Hydrogen bonds: B:K.241, B:P.292, D:G.258, D:A.259, D:G.327, D:G.329, D:L.330, D:D.356, D:N.359, D:N.359, D:H.378, D:G.380, D:G.440, D:D.443, D:D.443
- Water bridges: B:K.241
- Salt bridges: B:K.241, B:K.246, D:H.378, D:H.378, D:R.384
- pi-Stacking: B:H.240, B:H.240, D:H.378
NPW.30: 28 residues within 4Å:- Chain E: Y.256, G.258, A.259, G.327, P.328, G.329, L.330, A.355, D.356, N.359, H.378, P.379, G.380, E.381, R.384, G.439, G.440, D.443
- Chain H: H.240, K.241, G.242, K.246, P.292, E.293, L.294, I.295
- Ligands: MG.27, ATP.29
26 PLIP interactions:18 interactions with chain E, 8 interactions with chain H- Hydrogen bonds: E:G.258, E:A.259, E:G.327, E:G.329, E:L.330, E:D.356, E:N.359, E:N.359, E:G.380, E:E.381, E:G.440, E:D.443, E:D.443, H:K.241, H:P.292
- Water bridges: E:D.443, H:K.241
- Salt bridges: E:H.378, E:H.378, E:R.384, H:K.241, H:K.246
- pi-Stacking: E:H.378, H:H.240, H:H.240
- Hydrophobic interactions: H:I.295
NPW.36: 28 residues within 4Å:- Chain F: Y.256, G.258, A.259, G.327, P.328, G.329, L.330, A.355, D.356, N.359, H.378, P.379, G.380, E.381, R.384, G.439, G.440, D.443
- Chain G: H.240, K.241, G.242, K.246, P.292, E.293, L.294, I.295
- Ligands: MG.33, ATP.35
26 PLIP interactions:18 interactions with chain F, 8 interactions with chain G- Hydrogen bonds: F:G.258, F:A.259, F:G.327, F:G.329, F:L.330, F:D.356, F:N.359, F:N.359, F:G.380, F:E.381, F:G.440, F:D.443, F:D.443, G:K.241, G:P.292
- Water bridges: F:D.443, G:K.241
- Salt bridges: F:H.378, F:H.378, F:R.384, G:K.241, G:K.246
- pi-Stacking: F:H.378, G:H.240, G:H.240
- Hydrophobic interactions: G:I.295
NPW.42: 28 residues within 4Å:- Chain E: H.240, K.241, G.242, K.246, P.292, E.293, L.294, I.295
- Chain G: Y.256, G.258, A.259, G.327, P.328, G.329, L.330, A.355, D.356, N.359, H.378, P.379, G.380, E.381, R.384, G.439, G.440, D.443
- Ligands: MG.39, ATP.41
26 PLIP interactions:8 interactions with chain E, 18 interactions with chain G- Hydrophobic interactions: E:I.295
- Hydrogen bonds: E:K.241, E:P.292, G:G.258, G:A.259, G:G.327, G:G.329, G:L.330, G:D.356, G:N.359, G:N.359, G:G.380, G:E.381, G:G.440, G:D.443, G:D.443
- Water bridges: E:K.241, G:D.443
- Salt bridges: E:K.241, E:K.246, G:H.378, G:H.378, G:R.384
- pi-Stacking: E:H.240, E:H.240, G:H.378
NPW.48: 28 residues within 4Å:- Chain F: H.240, K.241, G.242, K.246, P.292, E.293, L.294, I.295
- Chain H: Y.256, G.258, A.259, G.327, P.328, G.329, L.330, A.355, D.356, N.359, H.378, P.379, G.380, E.381, R.384, G.439, G.440, D.443
- Ligands: MG.45, ATP.47
26 PLIP interactions:18 interactions with chain H, 8 interactions with chain F- Hydrogen bonds: H:G.258, H:A.259, H:G.327, H:G.329, H:L.330, H:D.356, H:N.359, H:N.359, H:G.380, H:E.381, H:G.440, H:D.443, H:D.443, F:K.241, F:P.292
- Water bridges: H:D.443, F:K.241
- Salt bridges: H:H.378, H:H.378, H:R.384, F:K.241, F:K.246
- pi-Stacking: H:H.378, F:H.240, F:H.240
- Hydrophobic interactions: F:I.295
- 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
- 2011-06-22
- Peptides
- Putative uncharacterized protein: 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 2.61 Å
- Oligo State
- homo-octamer
- Ligands
- 8 x ALA- TRP- LEU- PHE- GLU- ALA: Unknown peptide, probably from expression host(Non-covalent)
- 8 x K: POTASSIUM ION(Non-covalent)
- 8 x MG: MAGNESIUM ION(Non-functional Binders)
- 8 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)
- 8 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
- 8 x NPW: BETA-6-HYDROXY-1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE(Non-covalent)
- 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
- 2011-06-22
- Peptides
- Putative uncharacterized protein: ABCDEFGH
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
AE
AF
AG
AH
A