SMTL ID : 3rre.1

Crystal Structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima in complex with ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-octamer

Ligands

8 x ALA- ALA- TRP- LEU- PHE- GLU- ALA: peptide(Non-covalent)

ALA-ALA-TRP-LEU-PHE-GLU-ALA.1: 15 residues within 4Å: Chain A: R.34, S.38, L.41, A.42, E.45, L.203, K.204, V.205, A.206, N.207 Chain E: I.37, V.40, L.41, E.44, N.74 15 PLIP interactions: 7 interactions with chain A, 8 interactions with chain E Hydrophobic interactions: A:L.41, A:A.42, A:A.206, E:I.37, E:V.40, E:L.41, E:N.74 Hydrogen bonds: A:V.205, A:V.205, A:N.207, A:N.207, E:E.44, E:E.44, E:N.49 Water bridges: E:E.44 ALA-ALA-TRP-LEU-PHE-GLU-ALA.8: 15 residues within 4Å: Chain B: R.34, S.38, L.41, A.42, E.45, L.203, K.204, V.205, A.206, N.207 Chain F: I.37, V.40, L.41, E.44, N.74 15 PLIP interactions: 7 interactions with chain B, 8 interactions with chain F Hydrophobic interactions: B:L.41, B:A.42, B:A.206, F:I.37, F:V.40, F:L.41, F:N.74 Hydrogen bonds: B:V.205, B:V.205, B:N.207, B:N.207, F:E.44, F:E.44, F:N.49 Water bridges: F:E.44 ALA-ALA-TRP-LEU-PHE-GLU-ALA.15: 15 residues within 4Å: Chain C: R.34, S.38, L.41, A.42, E.45, L.203, K.204, V.205, A.206, N.207 Chain H: I.37, V.40, L.41, E.44, N.74 15 PLIP interactions: 7 interactions with chain C, 8 interactions with chain H Hydrophobic interactions: C:L.41, C:A.42, C:A.206, H:I.37, H:V.40, H:L.41, H:N.74 Hydrogen bonds: C:V.205, C:V.205, C:N.207, C:N.207, H:E.44, H:E.44, H:N.49 Water bridges: H:E.44 ALA-ALA-TRP-LEU-PHE-GLU-ALA.22: 15 residues within 4Å: Chain D: R.34, S.38, L.41, A.42, E.45, L.203, K.204, V.205, A.206, N.207 Chain G: I.37, V.40, L.41, E.44, N.74 15 PLIP interactions: 7 interactions with chain D, 8 interactions with chain G Hydrophobic interactions: D:L.41, D:A.42, D:A.206, G:I.37, G:V.40, G:L.41, G:N.74 Hydrogen bonds: D:V.205, D:V.205, D:N.207, D:N.207, G:E.44, G:E.44, G:N.49 Water bridges: G:E.44 ALA-ALA-TRP-LEU-PHE-GLU-ALA.29: 15 residues within 4Å: Chain A: I.37, V.40, L.41, E.44, N.74 Chain E: R.34, S.38, L.41, A.42, E.45, L.203, K.204, V.205, A.206, N.207 17 PLIP interactions: 7 interactions with chain E, 10 interactions with chain A Hydrophobic interactions: E:L.41, E:A.42, E:A.206, A:I.37, A:V.40, A:L.41, A:N.74 Hydrogen bonds: E:V.205, E:V.205, E:N.207, E:N.207, A:E.44, A:E.44, A:E.44, A:E.44, A:N.49 Water bridges: A:E.44 ALA-ALA-TRP-LEU-PHE-GLU-ALA.36: 15 residues within 4Å: Chain B: I.37, V.40, L.41, E.44, N.74 Chain F: R.34, S.38, L.41, A.42, E.45, L.203, K.204, V.205, A.206, N.207 17 PLIP interactions: 10 interactions with chain B, 7 interactions with chain F Hydrophobic interactions: B:I.37, B:V.40, B:L.41, B:N.74, F:L.41, F:A.42, F:A.206 Hydrogen bonds: B:E.44, B:E.44, B:E.44, B:E.44, B:N.49, F:V.205, F:V.205, F:N.207, F:N.207 Water bridges: B:E.44 ALA-ALA-TRP-LEU-PHE-GLU-ALA.43: 15 residues within 4Å: Chain D: I.37, V.40, L.41, E.44, N.74 Chain G: R.34, S.38, L.41, A.42, E.45, L.203, K.204, V.205, A.206, N.207 17 PLIP interactions: 10 interactions with chain D, 7 interactions with chain G Hydrophobic interactions: D:I.37, D:V.40, D:L.41, D:N.74, G:L.41, G:A.42, G:A.206 Hydrogen bonds: D:E.44, D:E.44, D:E.44, D:E.44, D:N.49, G:V.205, G:V.205, G:N.207, G:N.207 Water bridges: D:E.44 ALA-ALA-TRP-LEU-PHE-GLU-ALA.50: 15 residues within 4Å: Chain C: I.37, V.40, L.41, E.44, N.74 Chain H: R.34, S.38, L.41, A.42, E.45, L.203, K.204, V.205, A.206, N.207 17 PLIP interactions: 7 interactions with chain H, 10 interactions with chain C Hydrophobic interactions: H:L.41, H:A.42, H:A.206, C:I.37, C:V.40, C:L.41, C:N.74 Hydrogen bonds: H:V.205, H:V.205, H:N.207, H:N.207, C:E.44, C:E.44, C:E.44, C:E.44, C:N.49 Water bridges: C:E.44

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-functional Binders)

MG.3: 1 residues within 4Å: Ligands: ADP.4 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Ligands: ADP.11 No protein-ligand interaction detected (PLIP) MG.17: 1 residues within 4Å: Ligands: ADP.18 No protein-ligand interaction detected (PLIP) MG.24: 1 residues within 4Å: Ligands: ADP.25 No protein-ligand interaction detected (PLIP) MG.31: 1 residues within 4Å: Ligands: ADP.32 No protein-ligand interaction detected (PLIP) MG.38: 1 residues within 4Å: Ligands: ADP.39 No protein-ligand interaction detected (PLIP) MG.45: 1 residues within 4Å: Ligands: ADP.46 No protein-ligand interaction detected (PLIP) MG.52: 1 residues within 4Å: Ligands: ADP.53 No protein-ligand interaction detected (PLIP)

24 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.4: 21 residues within 4Å: Chain A: H.378, K.414, S.415, A.416, T.418, 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, ADP.6 17 PLIP interactions: 13 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:S.415, A:T.418, A:S.437, A:G.440, A:S.441, A:G.442, A:D.443, D:S.239 Water bridges: A:K.414, A:K.414, A:K.414, A:H.470, D:K.241 Salt bridges: A:H.378, A:K.414, D:K.241, D:K.241 ADP.5: 12 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 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.63, A:N.64, A:G.130, A:G.132, A:L.133, A:R.134, A:E.136 Water bridges: A:G.61, A:G.62, A:G.62, A:T.131, A:T.131 ADP.6: 10 residues within 4Å: Chain A: H.378, P.379, G.380, R.384, V.390, K.394, S.415 Chain D: H.240, K.241 Ligands: ADP.4 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:G.380, A:S.415 Water bridges: A:R.384, A:R.384, A:K.394 Salt bridges: A:H.378, A:H.378, A:R.384, D:K.241 pi-Stacking: D:H.240, D:H.240 ADP.11: 21 residues within 4Å: Chain B: H.378, K.414, S.415, A.416, T.418, 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, ADP.13 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:S.415, B:T.418, B:S.437, B:G.440, B:S.441, B:G.442, B:D.443, C:S.239 Water bridges: B:K.414, B:K.414, B:K.414, B:H.470, C:K.241 Salt bridges: B:H.378, B:K.414, C:K.241, C:K.241 ADP.12: 12 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 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:N.63, B:N.64, B:G.130, B:G.132, B:L.133, B:R.134, B:E.136 Water bridges: B:G.61, B:G.62, B:G.62, B:T.131, B:T.131 ADP.13: 10 residues within 4Å: Chain B: H.378, P.379, G.380, R.384, V.390, K.394, S.415 Chain C: H.240, K.241 Ligands: ADP.11 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:G.380, B:S.415 Water bridges: B:R.384, B:R.384, B:K.394 Salt bridges: B:H.378, B:H.378, B:R.384, C:K.241 pi-Stacking: C:H.240, C:H.240 ADP.18: 21 residues within 4Å: Chain A: R.237, S.239, K.241 Chain C: H.378, K.414, S.415, A.416, T.418, 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, ADP.20 17 PLIP interactions: 13 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:S.415, C:T.418, C:S.437, C:G.440, C:S.441, C:G.442, C:D.443, A:S.239 Water bridges: C:K.414, C:K.414, C:K.414, C:H.470, A:K.241 Salt bridges: C:H.378, C:K.414, A:K.241, A:K.241 ADP.19: 12 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 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:N.63, C:N.64, C:G.130, C:G.132, C:L.133, C:R.134, C:E.136 Water bridges: C:G.61, C:G.62, C:G.62, C:T.131, C:T.131 ADP.20: 10 residues within 4Å: Chain A: H.240, K.241 Chain C: H.378, P.379, G.380, R.384, V.390, K.394, S.415 Ligands: ADP.18 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:G.380, C:S.415 Water bridges: C:R.384, C:R.384, C:K.394 Salt bridges: C:H.378, C:H.378, C:R.384, A:K.241 pi-Stacking: A:H.240, A:H.240 ADP.25: 21 residues within 4Å: Chain B: R.237, S.239, K.241 Chain D: H.378, K.414, S.415, A.416, T.418, 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, ADP.27 17 PLIP interactions: 4 interactions with chain B, 13 interactions with chain D Hydrogen bonds: B:S.239, D:S.415, D:T.418, D:S.437, D:G.440, D:S.441, D:G.442, D:D.443 Water bridges: B:K.241, D:K.414, D:K.414, D:K.414, D:H.470 Salt bridges: B:K.241, B:K.241, D:H.378, D:K.414 ADP.26: 12 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 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:N.63, D:N.64, D:G.130, D:G.132, D:L.133, D:R.134, D:E.136 Water bridges: D:G.61, D:G.62, D:G.62, D:T.131, D:T.131 ADP.27: 10 residues within 4Å: Chain B: H.240, K.241 Chain D: H.378, P.379, G.380, R.384, V.390, K.394, S.415 Ligands: ADP.25 11 PLIP interactions: 3 interactions with chain B, 8 interactions with chain D Salt bridges: B:K.241, D:H.378, D:H.378, D:R.384 pi-Stacking: B:H.240, B:H.240 Hydrogen bonds: D:G.380, D:S.415 Water bridges: D:R.384, D:R.384, D:K.394 ADP.32: 21 residues within 4Å: Chain E: H.378, K.414, S.415, A.416, T.418, 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, ADP.34 17 PLIP interactions: 13 interactions with chain E, 4 interactions with chain H Hydrogen bonds: E:S.415, E:S.437, E:G.440, E:S.441, E:G.442, E:D.443, H:S.239 Water bridges: E:K.414, E:K.414, E:T.418, E:T.418, E:D.443, H:K.241 Salt bridges: E:H.378, E:K.414, H:K.241, H:K.241 ADP.33: 12 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 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:N.63, E:N.64, E:G.130, E:G.132, E:L.133, E:R.134, E:E.136 Water bridges: E:G.61, E:G.62, E:G.62 ADP.34: 10 residues within 4Å: Chain E: H.378, P.379, G.380, R.384, V.390, K.394, S.415 Chain H: H.240, K.241 Ligands: ADP.32 11 PLIP interactions: 3 interactions with chain H, 8 interactions with chain E Salt bridges: H:K.241, E:H.378, E:H.378, E:R.384 pi-Stacking: H:H.240, H:H.240 Hydrogen bonds: E:G.380, E:S.415 Water bridges: E:R.384, E:R.384, E:K.394 ADP.39: 21 residues within 4Å: Chain F: H.378, K.414, S.415, A.416, T.418, 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, ADP.41 17 PLIP interactions: 13 interactions with chain F, 4 interactions with chain G Hydrogen bonds: F:S.415, F:S.437, F:G.440, F:S.441, F:G.442, F:D.443, G:S.239 Water bridges: F:K.414, F:K.414, F:T.418, F:T.418, F:D.443, G:K.241 Salt bridges: F:H.378, F:K.414, G:K.241, G:K.241 ADP.40: 12 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 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:N.63, F:N.64, F:G.130, F:G.132, F:L.133, F:R.134, F:E.136 Water bridges: F:G.61, F:G.62, F:G.62 ADP.41: 10 residues within 4Å: Chain F: H.378, P.379, G.380, R.384, V.390, K.394, S.415 Chain G: H.240, K.241 Ligands: ADP.39 11 PLIP interactions: 8 interactions with chain F, 3 interactions with chain G Hydrogen bonds: F:G.380, F:S.415 Water bridges: F:R.384, F:R.384, F:K.394 Salt bridges: F:H.378, F:H.378, F:R.384, G:K.241 pi-Stacking: G:H.240, G:H.240 ADP.46: 21 residues within 4Å: Chain E: R.237, S.239, K.241 Chain G: H.378, K.414, S.415, A.416, T.418, 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, ADP.48 17 PLIP interactions: 13 interactions with chain G, 4 interactions with chain E Hydrogen bonds: G:S.415, G:S.437, G:G.440, G:S.441, G:G.442, G:D.443, E:S.239 Water bridges: G:K.414, G:K.414, G:T.418, G:T.418, G:D.443, E:K.241 Salt bridges: G:H.378, G:K.414, E:K.241, E:K.241 ADP.47: 12 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 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:N.63, G:N.64, G:G.130, G:G.132, G:L.133, G:R.134, G:E.136 Water bridges: G:G.61, G:G.62, G:G.62 ADP.48: 10 residues within 4Å: Chain E: H.240, K.241 Chain G: H.378, P.379, G.380, R.384, V.390, K.394, S.415 Ligands: ADP.46 11 PLIP interactions: 8 interactions with chain G, 3 interactions with chain E Hydrogen bonds: G:G.380, G:S.415 Water bridges: G:R.384, G:R.384, G:K.394 Salt bridges: G:H.378, G:H.378, G:R.384, E:K.241 pi-Stacking: E:H.240, E:H.240 ADP.53: 21 residues within 4Å: Chain F: R.237, S.239, K.241 Chain H: H.378, K.414, S.415, A.416, T.418, 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, ADP.55 17 PLIP interactions: 13 interactions with chain H, 4 interactions with chain F Hydrogen bonds: H:S.415, H:S.437, H:G.440, H:S.441, H:G.442, H:D.443, F:S.239 Water bridges: H:K.414, H:K.414, H:T.418, H:T.418, H:D.443, F:K.241 Salt bridges: H:H.378, H:K.414, F:K.241, F:K.241 ADP.54: 12 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 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:N.63, H:N.64, H:G.130, H:G.132, H:L.133, H:R.134, H:E.136 Water bridges: H:G.61, H:G.62, H:G.62 ADP.55: 10 residues within 4Å: Chain F: H.240, K.241 Chain H: H.378, P.379, G.380, R.384, V.390, K.394, S.415 Ligands: ADP.53 11 PLIP interactions: 8 interactions with chain H, 3 interactions with chain F Hydrogen bonds: H:G.380, H:S.415 Water bridges: H:R.384, H:R.384, H:K.394 Salt bridges: H:H.378, H:H.378, H:R.384, F:K.241 pi-Stacking: F:H.240, F:H.240

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: D.17, M.32, A.35, D.67, F.184, I.208 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.17 GOL.14: 6 residues within 4Å: Chain B: D.17, M.32, A.35, D.67, F.184, I.208 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.17 GOL.21: 6 residues within 4Å: Chain C: D.17, M.32, A.35, D.67, F.184, I.208 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.17 GOL.28: 6 residues within 4Å: Chain D: D.17, M.32, A.35, D.67, F.184, I.208 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.17 GOL.35: 6 residues within 4Å: Chain E: D.17, M.32, A.35, D.67, F.184, I.208 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.17 GOL.42: 6 residues within 4Å: Chain F: D.17, M.32, A.35, D.67, F.184, I.208 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:D.17 GOL.49: 6 residues within 4Å: Chain G: D.17, M.32, A.35, D.67, F.184, I.208 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:D.17 GOL.56: 6 residues within 4Å: Chain H: D.17, M.32, A.35, D.67, F.184, I.208 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:D.17

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
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

Bifunctional NAD(P)H-hydrate repair enzyme Nnr

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