- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.10 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: 6 residues within 4Å:- Chain A: N.64, D.126, 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.9: 6 residues within 4Å:- Chain B: N.64, D.126, 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.16: 6 residues within 4Å:- Chain C: N.64, D.126, 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.23: 6 residues within 4Å:- Chain D: N.64, D.126, 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.30: 6 residues within 4Å:- Chain E: N.64, D.126, 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.37: 6 residues within 4Å:- Chain F: N.64, D.126, 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.44: 6 residues within 4Å:- Chain G: N.64, D.126, 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.51: 6 residues within 4Å:- Chain H: N.64, D.126, 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: APR.5
No protein-ligand interaction detected (PLIP)MG.10: 2 residues within 4Å:- Chain B: K.414
- Ligands: APR.12
No protein-ligand interaction detected (PLIP)MG.17: 2 residues within 4Å:- Chain C: K.414
- Ligands: APR.19
No protein-ligand interaction detected (PLIP)MG.24: 2 residues within 4Å:- Chain D: K.414
- Ligands: APR.26
No protein-ligand interaction detected (PLIP)MG.31: 2 residues within 4Å:- Chain E: K.414
- Ligands: APR.33
No protein-ligand interaction detected (PLIP)MG.38: 2 residues within 4Å:- Chain F: K.414
- Ligands: APR.40
No protein-ligand interaction detected (PLIP)MG.45: 2 residues within 4Å:- Chain G: K.414
- Ligands: APR.47
No protein-ligand interaction detected (PLIP)MG.52: 2 residues within 4Å:- Chain H: K.414
- Ligands: APR.54
No protein-ligand interaction detected (PLIP)- 24 x APR: ADENOSINE-5-DIPHOSPHORIBOSE(Non-covalent)
APR.4: 16 residues within 4Å:- Chain A: D.17, G.61, G.62, N.63, N.64, D.67, F.129, G.130, T.131, G.132, L.133, R.134, G.135, E.136, Y.141, D.159
18 PLIP interactions:18 interactions with chain A- Hydrogen bonds: A:N.63, A:N.64, A:N.64, A:D.67, A:G.130, A:T.131, A:G.132, A:L.133, A:R.134, A:E.136, A:D.159
- Water bridges: A:G.61, A:G.61, A:G.62, A:D.67, A:K.90, A:T.131, A:T.131
APR.5: 25 residues within 4Å:- Chain A: A.355, H.378, E.381, K.414, S.415, A.416, T.418, G.432, N.433, T.434, L.436, S.437, 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, APR.6, GOL.7
27 PLIP interactions:21 interactions with chain A, 6 interactions with chain D- Hydrogen bonds: A:E.381, A:S.415, A:S.415, A:T.418, A:S.437, A:G.440, A:S.441, A:G.442, A:D.443, D:S.239, D:K.241
- Water bridges: A:G.329, A:D.356, A:H.378, A:E.381, A:K.414, A:K.414, A:K.414, A:K.438, A:S.441, A:H.470, D:K.241
- Salt bridges: A:H.378, A:K.414, D:K.241, D:K.241, D:K.241
APR.6: 13 residues within 4Å:- Chain A: Y.256, H.378, P.379, G.380, R.384, V.390, K.394, S.415
- Chain D: H.240, K.241, L.274, K.276
- Ligands: APR.5
16 PLIP interactions:8 interactions with chain D, 8 interactions with chain A- Hydrogen bonds: D:K.276, D:K.276, A:Y.256, A:G.380, A:S.415
- Water bridges: D:K.241, A:R.384, A:R.384, A:K.394
- Salt bridges: D:K.241, D:K.241, D:K.276, A:H.378, A:R.384
- pi-Stacking: D:H.240, D:H.240
APR.11: 16 residues within 4Å:- Chain B: D.17, G.61, G.62, N.63, N.64, D.67, F.129, G.130, T.131, G.132, L.133, R.134, G.135, E.136, Y.141, D.159
18 PLIP interactions:18 interactions with chain B- Hydrogen bonds: B:N.63, B:N.64, B:N.64, B:D.67, B:G.130, B:T.131, B:G.132, B:L.133, B:R.134, B:E.136, B:D.159
- Water bridges: B:G.61, B:G.61, B:G.62, B:D.67, B:K.90, B:T.131, B:T.131
APR.12: 25 residues within 4Å:- Chain B: A.355, H.378, E.381, K.414, S.415, A.416, T.418, G.432, N.433, T.434, L.436, S.437, G.439, G.440, S.441, G.442, D.443, L.445, H.470
- Chain C: R.237, S.239, K.241
- Ligands: MG.10, APR.13, GOL.14
27 PLIP interactions:21 interactions with chain B, 6 interactions with chain C- Hydrogen bonds: B:E.381, B:S.415, B:S.415, B:T.418, B:S.437, B:G.440, B:S.441, B:G.442, B:D.443, C:S.239, C:K.241
- Water bridges: B:G.329, B:D.356, B:H.378, B:E.381, B:K.414, B:K.414, B:K.414, B:K.438, B:S.441, B:H.470, C:K.241
- Salt bridges: B:H.378, B:K.414, C:K.241, C:K.241, C:K.241
APR.13: 13 residues within 4Å:- Chain B: Y.256, H.378, P.379, G.380, R.384, V.390, K.394, S.415
- Chain C: H.240, K.241, L.274, K.276
- Ligands: APR.12
16 PLIP interactions:8 interactions with chain B, 8 interactions with chain C- Hydrogen bonds: B:Y.256, B:G.380, B:S.415, C:K.276, C:K.276
- Water bridges: B:R.384, B:R.384, B:K.394, C:K.241
- Salt bridges: B:H.378, B:R.384, C:K.241, C:K.241, C:K.276
- pi-Stacking: C:H.240, C:H.240
APR.18: 16 residues within 4Å:- Chain C: D.17, G.61, G.62, N.63, N.64, D.67, F.129, G.130, T.131, G.132, L.133, R.134, G.135, E.136, Y.141, D.159
18 PLIP interactions:18 interactions with chain C- Hydrogen bonds: C:N.63, C:N.64, C:N.64, C:D.67, C:G.130, C:T.131, C:G.132, C:L.133, C:R.134, C:E.136, C:D.159
- Water bridges: C:G.61, C:G.61, C:G.62, C:D.67, C:K.90, C:T.131, C:T.131
APR.19: 25 residues within 4Å:- Chain A: R.237, S.239, K.241
- Chain C: A.355, H.378, E.381, K.414, S.415, A.416, T.418, G.432, N.433, T.434, L.436, S.437, G.439, G.440, S.441, G.442, D.443, L.445, H.470
- Ligands: MG.17, APR.20, GOL.21
27 PLIP interactions:21 interactions with chain C, 6 interactions with chain A- Hydrogen bonds: C:E.381, C:S.415, C:S.415, C:T.418, C:S.437, C:G.440, C:S.441, C:G.442, C:D.443, A:S.239, A:K.241
- Water bridges: C:G.329, C:D.356, C:H.378, C:E.381, C:K.414, C:K.414, C:K.414, C:K.438, C:S.441, C:H.470, A:K.241
- Salt bridges: C:H.378, C:K.414, A:K.241, A:K.241, A:K.241
APR.20: 13 residues within 4Å:- Chain A: H.240, K.241, L.274, K.276
- Chain C: Y.256, H.378, P.379, G.380, R.384, V.390, K.394, S.415
- Ligands: APR.19
16 PLIP interactions:8 interactions with chain C, 8 interactions with chain A- Hydrogen bonds: C:Y.256, C:G.380, C:S.415, A:K.276, A:K.276
- Water bridges: C:R.384, C:R.384, C:K.394, A:K.241
- Salt bridges: C:H.378, C:R.384, A:K.241, A:K.241, A:K.276
- pi-Stacking: A:H.240, A:H.240
APR.25: 16 residues within 4Å:- Chain D: D.17, G.61, G.62, N.63, N.64, D.67, F.129, G.130, T.131, G.132, L.133, R.134, G.135, E.136, Y.141, D.159
18 PLIP interactions:18 interactions with chain D- Hydrogen bonds: D:N.63, D:N.64, D:N.64, D:D.67, D:G.130, D:T.131, D:G.132, D:L.133, D:R.134, D:E.136, D:D.159
- Water bridges: D:G.61, D:G.61, D:G.62, D:D.67, D:K.90, D:T.131, D:T.131
APR.26: 25 residues within 4Å:- Chain B: R.237, S.239, K.241
- Chain D: A.355, H.378, E.381, K.414, S.415, A.416, T.418, G.432, N.433, T.434, L.436, S.437, G.439, G.440, S.441, G.442, D.443, L.445, H.470
- Ligands: MG.24, APR.27, GOL.28
27 PLIP interactions:21 interactions with chain D, 6 interactions with chain B- Hydrogen bonds: D:E.381, D:S.415, D:S.415, D:T.418, D:S.437, D:G.440, D:S.441, D:G.442, D:D.443, B:S.239, B:K.241
- Water bridges: D:G.329, D:D.356, D:H.378, D:E.381, D:K.414, D:K.414, D:K.414, D:K.438, D:S.441, D:H.470, B:K.241
- Salt bridges: D:H.378, D:K.414, B:K.241, B:K.241, B:K.241
APR.27: 13 residues within 4Å:- Chain B: H.240, K.241, L.274, K.276
- Chain D: Y.256, H.378, P.379, G.380, R.384, V.390, K.394, S.415
- Ligands: APR.26
16 PLIP interactions:8 interactions with chain D, 8 interactions with chain B- Hydrogen bonds: D:Y.256, D:G.380, D:S.415, B:K.276, B:K.276
- Water bridges: D:R.384, D:R.384, D:K.394, B:K.241
- Salt bridges: D:H.378, D:R.384, B:K.241, B:K.241, B:K.276
- pi-Stacking: B:H.240, B:H.240
APR.32: 16 residues within 4Å:- Chain E: D.17, G.61, G.62, N.63, N.64, D.67, F.129, G.130, T.131, G.132, L.133, R.134, G.135, 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:G.132, E:L.133, E:R.134, E:E.136, E:D.159, E:D.159
- Water bridges: E:G.61, E:G.61, E:G.62, E:D.67, E:K.90
APR.33: 25 residues within 4Å:- Chain E: A.355, H.378, E.381, K.414, S.415, A.416, T.418, G.432, N.433, T.434, L.436, S.437, G.439, G.440, S.441, G.442, D.443, L.445, H.470
- Chain H: R.237, S.239, K.241
- Ligands: MG.31, APR.34, GOL.35
27 PLIP interactions:21 interactions with chain E, 6 interactions with chain H- Hydrogen bonds: E:E.381, E:S.415, E:S.415, E:S.437, E:G.440, E:S.441, E:G.442, E:D.443, H:S.239, H:K.241
- Water bridges: E:G.329, E:D.356, E:H.378, E:E.381, E:K.414, E:K.414, E:K.414, E:T.418, E:T.418, E:K.438, E:S.441, H:K.241
- Salt bridges: E:H.378, E:K.414, H:K.241, H:K.241, H:K.241
APR.34: 13 residues within 4Å:- Chain E: Y.256, H.378, P.379, G.380, R.384, V.390, K.394, S.415
- Chain H: H.240, K.241, L.274, K.276
- Ligands: APR.33
17 PLIP interactions:9 interactions with chain E, 8 interactions with chain H- Hydrogen bonds: E:Y.256, E:Y.256, E:G.380, E:S.415, H:K.276, H:K.276
- Water bridges: E:E.381, E:R.384, E:K.394, H:K.241
- Salt bridges: E:H.378, E:R.384, H:K.241, H:K.241, H:K.276
- pi-Stacking: H:H.240, H:H.240
APR.39: 16 residues within 4Å:- Chain F: D.17, G.61, G.62, N.63, N.64, D.67, F.129, G.130, T.131, G.132, L.133, R.134, G.135, 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:G.132, F:L.133, F:R.134, F:E.136, F:D.159, F:D.159
- Water bridges: F:G.61, F:G.61, F:G.62, F:D.67, F:K.90
APR.40: 25 residues within 4Å:- Chain F: A.355, H.378, E.381, K.414, S.415, A.416, T.418, G.432, N.433, T.434, L.436, S.437, G.439, G.440, S.441, G.442, D.443, L.445, H.470
- Chain G: R.237, S.239, K.241
- Ligands: MG.38, APR.41, GOL.42
27 PLIP interactions:21 interactions with chain F, 6 interactions with chain G- Hydrogen bonds: F:E.381, F:S.415, F:S.415, F:S.437, F:G.440, F:S.441, F:G.442, F:D.443, G:S.239, G:K.241
- Water bridges: F:G.329, F:D.356, F:H.378, F:E.381, F:K.414, F:K.414, F:K.414, F:T.418, F:T.418, F:K.438, F:S.441, G:K.241
- Salt bridges: F:H.378, F:K.414, G:K.241, G:K.241, G:K.241
APR.41: 13 residues within 4Å:- Chain F: Y.256, H.378, P.379, G.380, R.384, V.390, K.394, S.415
- Chain G: H.240, K.241, L.274, K.276
- Ligands: APR.40
17 PLIP interactions:9 interactions with chain F, 8 interactions with chain G- Hydrogen bonds: F:Y.256, F:Y.256, F:G.380, F:S.415, G:K.276, G:K.276
- Water bridges: F:E.381, F:R.384, F:K.394, G:K.241
- Salt bridges: F:H.378, F:R.384, G:K.241, G:K.241, G:K.276
- pi-Stacking: G:H.240, G:H.240
APR.46: 16 residues within 4Å:- Chain G: D.17, G.61, G.62, N.63, N.64, D.67, F.129, G.130, T.131, G.132, L.133, R.134, G.135, 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:G.132, G:L.133, G:R.134, G:E.136, G:D.159, G:D.159
- Water bridges: G:G.61, G:G.61, G:G.62, G:D.67, G:K.90
APR.47: 25 residues within 4Å:- Chain E: R.237, S.239, K.241
- Chain G: A.355, H.378, E.381, K.414, S.415, A.416, T.418, G.432, N.433, T.434, L.436, S.437, G.439, G.440, S.441, G.442, D.443, L.445, H.470
- Ligands: MG.45, APR.48, GOL.49
27 PLIP interactions:21 interactions with chain G, 6 interactions with chain E- Hydrogen bonds: G:E.381, G:S.415, G:S.415, G:S.437, G:G.440, G:S.441, G:G.442, G:D.443, E:S.239, E:K.241
- Water bridges: G:G.329, G:D.356, G:H.378, G:E.381, G:K.414, G:K.414, G:K.414, G:T.418, G:T.418, G:K.438, G:S.441, E:K.241
- Salt bridges: G:H.378, G:K.414, E:K.241, E:K.241, E:K.241
APR.48: 13 residues within 4Å:- Chain E: H.240, K.241, L.274, K.276
- Chain G: Y.256, H.378, P.379, G.380, R.384, V.390, K.394, S.415
- Ligands: APR.47
17 PLIP interactions:9 interactions with chain G, 8 interactions with chain E- Hydrogen bonds: G:Y.256, G:Y.256, G:G.380, G:S.415, E:K.276, E:K.276
- Water bridges: G:E.381, G:R.384, G:K.394, E:K.241
- Salt bridges: G:H.378, G:R.384, E:K.241, E:K.241, E:K.276
- pi-Stacking: E:H.240, E:H.240
APR.53: 16 residues within 4Å:- Chain H: D.17, G.61, G.62, N.63, N.64, D.67, F.129, G.130, T.131, G.132, L.133, R.134, G.135, 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:G.132, H:L.133, H:R.134, H:E.136, H:D.159, H:D.159
- Water bridges: H:G.61, H:G.61, H:G.62, H:D.67, H:K.90
APR.54: 25 residues within 4Å:- Chain F: R.237, S.239, K.241
- Chain H: A.355, H.378, E.381, K.414, S.415, A.416, T.418, G.432, N.433, T.434, L.436, S.437, G.439, G.440, S.441, G.442, D.443, L.445, H.470
- Ligands: MG.52, APR.55, GOL.56
27 PLIP interactions:21 interactions with chain H, 6 interactions with chain F- Hydrogen bonds: H:E.381, H:S.415, H:S.415, H:S.437, H:G.440, H:S.441, H:G.442, H:D.443, F:S.239, F:K.241
- Water bridges: H:G.329, H:D.356, H:H.378, H:E.381, H:K.414, H:K.414, H:K.414, H:T.418, H:T.418, H:K.438, H:S.441, F:K.241
- Salt bridges: H:H.378, H:K.414, F:K.241, F:K.241, F:K.241
APR.55: 13 residues within 4Å:- Chain F: H.240, K.241, L.274, K.276
- Chain H: Y.256, H.378, P.379, G.380, R.384, V.390, K.394, S.415
- Ligands: APR.54
17 PLIP interactions:9 interactions with chain H, 8 interactions with chain F- Hydrogen bonds: H:Y.256, H:Y.256, H:G.380, H:S.415, F:K.276, F:K.276
- Water bridges: H:E.381, H:R.384, H:K.394, F:K.241
- Salt bridges: H:H.378, H:R.384, F:K.241, F:K.241, F:K.276
- pi-Stacking: F:H.240, F:H.240
- 8 x GOL: GLYCEROL(Non-functional Binders)
GOL.7: 9 residues within 4Å:- Chain A: G.258, A.259, L.262, G.439, G.440, D.443
- Chain D: P.292, E.293
- Ligands: APR.5
6 PLIP interactions:4 interactions with chain A, 2 interactions with chain D- Hydrogen bonds: A:D.443, D:P.292
- Water bridges: A:G.258, A:D.443, A:D.443, D:I.295
GOL.14: 9 residues within 4Å:- Chain B: G.258, A.259, L.262, G.439, G.440, D.443
- Chain C: P.292, E.293
- Ligands: APR.12
6 PLIP interactions:4 interactions with chain B, 2 interactions with chain C- Hydrogen bonds: B:D.443, C:P.292
- Water bridges: B:G.258, B:D.443, B:D.443, C:I.295
GOL.21: 9 residues within 4Å:- Chain A: P.292, E.293
- Chain C: G.258, A.259, L.262, G.439, G.440, D.443
- Ligands: APR.19
6 PLIP interactions:2 interactions with chain A, 4 interactions with chain C- Hydrogen bonds: A:P.292, C:D.443
- Water bridges: A:I.295, C:G.258, C:D.443, C:D.443
GOL.28: 9 residues within 4Å:- Chain B: P.292, E.293
- Chain D: G.258, A.259, L.262, G.439, G.440, D.443
- Ligands: APR.26
6 PLIP interactions:4 interactions with chain D, 2 interactions with chain B- Hydrogen bonds: D:D.443, B:P.292
- Water bridges: D:G.258, D:D.443, D:D.443, B:I.295
GOL.35: 9 residues within 4Å:- Chain E: G.258, A.259, L.262, G.439, G.440, D.443
- Chain H: P.292, E.293
- Ligands: APR.33
5 PLIP interactions:2 interactions with chain H, 3 interactions with chain E- Hydrogen bonds: H:P.292
- Water bridges: H:I.295, E:G.258, E:D.443, E:D.443
GOL.42: 9 residues within 4Å:- Chain F: G.258, A.259, L.262, G.439, G.440, D.443
- Chain G: P.292, E.293
- Ligands: APR.40
5 PLIP interactions:2 interactions with chain G, 3 interactions with chain F- Hydrogen bonds: G:P.292
- Water bridges: G:I.295, F:G.258, F:D.443, F:D.443
GOL.49: 9 residues within 4Å:- Chain E: P.292, E.293
- Chain G: G.258, A.259, L.262, G.439, G.440, D.443
- Ligands: APR.47
5 PLIP interactions:2 interactions with chain E, 3 interactions with chain G- Hydrogen bonds: E:P.292
- Water bridges: E:I.295, G:G.258, G:D.443, G:D.443
GOL.56: 9 residues within 4Å:- Chain F: P.292, E.293
- Chain H: G.258, A.259, L.262, G.439, G.440, D.443
- Ligands: APR.54
5 PLIP interactions:3 interactions with chain H, 2 interactions with chain F- Water bridges: H:G.258, H:D.443, H:D.443, F:I.295
- Hydrogen bonds: F:P.292
- 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 2.10 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-covalent)
- 24 x APR: ADENOSINE-5-DIPHOSPHORIBOSE(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
- 2011-06-22
- Peptides
- Putative uncharacterized protein: ABCDEFGH
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
AE
AF
AG
AH
A