SMTL ID : 2w8r.1 (2 other biounits)

The crystal structure of human SSADH in complex with NAD+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-12-mer

Ligands

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

ADP.1: 14 residues within 4Å: Chain A: I.153, T.154, P.155, W.156, K.180, P.181, A.182, E.183, A.216, K.217, G.220, F.234, S.237, T.240 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.154, A:K.180, A:E.183, A:S.237 ADP.14: 14 residues within 4Å: Chain B: I.153, T.154, P.155, W.156, K.180, P.181, A.182, E.183, A.216, K.217, G.220, F.234, S.237, T.240 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.154, B:K.180, B:E.183, B:S.237, B:T.240 ADP.27: 14 residues within 4Å: Chain C: I.153, T.154, P.155, W.156, K.180, P.181, A.182, E.183, A.216, K.217, G.220, F.234, S.237, T.240 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.154, C:K.180, C:E.183, C:S.237 ADP.40: 14 residues within 4Å: Chain D: I.153, T.154, P.155, W.156, K.180, P.181, A.182, E.183, A.216, K.217, G.220, F.234, S.237, T.240 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.154, D:K.180, D:E.183, D:S.237 ADP.53: 14 residues within 4Å: Chain E: I.153, T.154, P.155, W.156, K.180, P.181, A.182, E.183, A.216, K.217, G.220, F.234, S.237, T.240 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:T.154, E:K.180, E:E.183, E:S.237 ADP.66: 14 residues within 4Å: Chain F: I.153, T.154, P.155, W.156, K.180, P.181, A.182, E.183, A.216, K.217, G.220, F.234, S.237, T.240 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:T.154, F:K.180, F:E.183, F:S.237, F:T.240 ADP.79: 14 residues within 4Å: Chain G: I.153, T.154, P.155, W.156, K.180, P.181, A.182, E.183, A.216, K.217, G.220, F.234, S.237, T.240 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:T.154, G:K.180, G:E.183, G:S.237, G:T.240 ADP.92: 14 residues within 4Å: Chain H: I.153, T.154, P.155, W.156, K.180, P.181, A.182, E.183, A.216, K.217, G.220, F.234, S.237, T.240 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:T.154, H:K.180, H:E.183, H:S.237 ADP.105: 14 residues within 4Å: Chain I: I.153, T.154, P.155, W.156, K.180, P.181, A.182, E.183, A.216, K.217, G.220, F.234, S.237, T.240 5 PLIP interactions: 5 interactions with chain I Hydrogen bonds: I:T.154, I:K.180, I:E.183, I:S.237, I:T.240 ADP.118: 14 residues within 4Å: Chain J: I.153, T.154, P.155, W.156, K.180, P.181, A.182, E.183, A.216, K.217, G.220, F.234, S.237, T.240 5 PLIP interactions: 5 interactions with chain J Hydrogen bonds: J:T.154, J:K.180, J:E.183, J:S.237, J:T.240 ADP.131: 14 residues within 4Å: Chain K: I.153, T.154, P.155, W.156, K.180, P.181, A.182, E.183, A.216, K.217, G.220, F.234, S.237, T.240 5 PLIP interactions: 5 interactions with chain K Hydrogen bonds: K:T.154, K:K.180, K:E.183, K:S.237, K:T.240 ADP.144: 14 residues within 4Å: Chain L: I.153, T.154, P.155, W.156, K.180, P.181, A.182, E.183, A.216, K.217, G.220, F.234, S.237, T.240 4 PLIP interactions: 4 interactions with chain L Hydrogen bonds: L:T.154, L:K.180, L:E.183, L:S.237

120 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: L.320, R.321, V.322, H.365 Ligand excluded by PLIP SO4.3: 4 residues within 4Å: Chain A: Q.301, D.402, T.403, E.404 Ligand excluded by PLIP SO4.4: 4 residues within 4Å: Chain A: R.20 Chain C: L.3, S.35, A.37 Ligand excluded by PLIP SO4.5: 2 residues within 4Å: Chain A: R.302, K.400 Ligand excluded by PLIP SO4.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.7: 7 residues within 4Å: Chain A: G.107, E.108, Y.111, F.158, R.286, S.450 Ligands: SO4.11 Ligand excluded by PLIP SO4.8: 5 residues within 4Å: Chain A: R.213, K.214 Chain E: G.46, V.47, R.48 Ligand excluded by PLIP SO4.9: 8 residues within 4Å: Chain A: V.17, G.18, R.20, L.22, A.56 Chain C: Q.31, G.36, K.369 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain A: R.12, W.21 Ligand excluded by PLIP SO4.11: 8 residues within 4Å: Chain A: Y.111, F.158, R.165, R.286, V.293, S.450, F.456 Ligands: SO4.7 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain B: L.320, R.321, V.322, H.365 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain B: Q.301, D.402, T.403, E.404 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain B: R.20 Chain I: L.3, S.35, A.37 Ligand excluded by PLIP SO4.18: 2 residues within 4Å: Chain B: R.302, K.400 Ligand excluded by PLIP SO4.19: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.20: 7 residues within 4Å: Chain B: G.107, E.108, Y.111, F.158, R.286, S.450 Ligands: SO4.24 Ligand excluded by PLIP SO4.21: 5 residues within 4Å: Chain B: R.213, K.214 Chain G: G.46, V.47, R.48 Ligand excluded by PLIP SO4.22: 8 residues within 4Å: Chain B: V.17, G.18, R.20, L.22, A.56 Chain I: Q.31, G.36, K.369 Ligand excluded by PLIP SO4.23: 2 residues within 4Å: Chain B: R.12, W.21 Ligand excluded by PLIP SO4.24: 8 residues within 4Å: Chain B: Y.111, F.158, R.165, R.286, V.293, S.450, F.456 Ligands: SO4.20 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain C: L.320, R.321, V.322, H.365 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain C: Q.301, D.402, T.403, E.404 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain C: R.20 Chain E: L.3, S.35, A.37 Ligand excluded by PLIP SO4.31: 2 residues within 4Å: Chain C: R.302, K.400 Ligand excluded by PLIP SO4.32: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.33: 7 residues within 4Å: Chain C: G.107, E.108, Y.111, F.158, R.286, S.450 Ligands: SO4.37 Ligand excluded by PLIP SO4.34: 5 residues within 4Å: Chain A: G.46, V.47, R.48 Chain C: R.213, K.214 Ligand excluded by PLIP SO4.35: 8 residues within 4Å: Chain C: V.17, G.18, R.20, L.22, A.56 Chain E: Q.31, G.36, K.369 Ligand excluded by PLIP SO4.36: 2 residues within 4Å: Chain C: R.12, W.21 Ligand excluded by PLIP SO4.37: 8 residues within 4Å: Chain C: Y.111, F.158, R.165, R.286, V.293, S.450, F.456 Ligands: SO4.33 Ligand excluded by PLIP SO4.41: 4 residues within 4Å: Chain D: L.320, R.321, V.322, H.365 Ligand excluded by PLIP SO4.42: 4 residues within 4Å: Chain D: Q.301, D.402, T.403, E.404 Ligand excluded by PLIP SO4.43: 4 residues within 4Å: Chain D: R.20 Chain H: L.3, S.35, A.37 Ligand excluded by PLIP SO4.44: 2 residues within 4Å: Chain D: R.302, K.400 Ligand excluded by PLIP SO4.45: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.46: 7 residues within 4Å: Chain D: G.107, E.108, Y.111, F.158, R.286, S.450 Ligands: SO4.50 Ligand excluded by PLIP SO4.47: 5 residues within 4Å: Chain D: R.213, K.214 Chain L: G.46, V.47, R.48 Ligand excluded by PLIP SO4.48: 8 residues within 4Å: Chain D: V.17, G.18, R.20, L.22, A.56 Chain H: Q.31, G.36, K.369 Ligand excluded by PLIP SO4.49: 2 residues within 4Å: Chain D: R.12, W.21 Ligand excluded by PLIP SO4.50: 8 residues within 4Å: Chain D: Y.111, F.158, R.165, R.286, V.293, S.450, F.456 Ligands: SO4.46 Ligand excluded by PLIP SO4.54: 4 residues within 4Å: Chain E: L.320, R.321, V.322, H.365 Ligand excluded by PLIP SO4.55: 4 residues within 4Å: Chain E: Q.301, D.402, T.403, E.404 Ligand excluded by PLIP SO4.56: 4 residues within 4Å: Chain A: L.3, S.35, A.37 Chain E: R.20 Ligand excluded by PLIP SO4.57: 2 residues within 4Å: Chain E: R.302, K.400 Ligand excluded by PLIP SO4.58: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.59: 7 residues within 4Å: Chain E: G.107, E.108, Y.111, F.158, R.286, S.450 Ligands: SO4.63 Ligand excluded by PLIP SO4.60: 5 residues within 4Å: Chain C: G.46, V.47, R.48 Chain E: R.213, K.214 Ligand excluded by PLIP SO4.61: 8 residues within 4Å: Chain A: Q.31, G.36, K.369 Chain E: V.17, G.18, R.20, L.22, A.56 Ligand excluded by PLIP SO4.62: 2 residues within 4Å: Chain E: R.12, W.21 Ligand excluded by PLIP SO4.63: 8 residues within 4Å: Chain E: Y.111, F.158, R.165, R.286, V.293, S.450, F.456 Ligands: SO4.59 Ligand excluded by PLIP SO4.67: 4 residues within 4Å: Chain F: L.320, R.321, V.322, H.365 Ligand excluded by PLIP SO4.68: 4 residues within 4Å: Chain F: Q.301, D.402, T.403, E.404 Ligand excluded by PLIP SO4.69: 4 residues within 4Å: Chain F: R.20 Chain K: L.3, S.35, A.37 Ligand excluded by PLIP SO4.70: 2 residues within 4Å: Chain F: R.302, K.400 Ligand excluded by PLIP SO4.71: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.72: 7 residues within 4Å: Chain F: G.107, E.108, Y.111, F.158, R.286, S.450 Ligands: SO4.76 Ligand excluded by PLIP SO4.73: 5 residues within 4Å: Chain F: R.213, K.214 Chain J: G.46, V.47, R.48 Ligand excluded by PLIP SO4.74: 8 residues within 4Å: Chain F: V.17, G.18, R.20, L.22, A.56 Chain K: Q.31, G.36, K.369 Ligand excluded by PLIP SO4.75: 2 residues within 4Å: Chain F: R.12, W.21 Ligand excluded by PLIP SO4.76: 8 residues within 4Å: Chain F: Y.111, F.158, R.165, R.286, V.293, S.450, F.456 Ligands: SO4.72 Ligand excluded by PLIP SO4.80: 4 residues within 4Å: Chain G: L.320, R.321, V.322, H.365 Ligand excluded by PLIP SO4.81: 4 residues within 4Å: Chain G: Q.301, D.402, T.403, E.404 Ligand excluded by PLIP SO4.82: 4 residues within 4Å: Chain B: L.3, S.35, A.37 Chain G: R.20 Ligand excluded by PLIP SO4.83: 2 residues within 4Å: Chain G: R.302, K.400 Ligand excluded by PLIP SO4.84: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.85: 7 residues within 4Å: Chain G: G.107, E.108, Y.111, F.158, R.286, S.450 Ligands: SO4.89 Ligand excluded by PLIP SO4.86: 5 residues within 4Å: Chain G: R.213, K.214 Chain I: G.46, V.47, R.48 Ligand excluded by PLIP SO4.87: 8 residues within 4Å: Chain B: Q.31, G.36, K.369 Chain G: V.17, G.18, R.20, L.22, A.56 Ligand excluded by PLIP SO4.88: 2 residues within 4Å: Chain G: R.12, W.21 Ligand excluded by PLIP SO4.89: 8 residues within 4Å: Chain G: Y.111, F.158, R.165, R.286, V.293, S.450, F.456 Ligands: SO4.85 Ligand excluded by PLIP SO4.93: 4 residues within 4Å: Chain H: L.320, R.321, V.322, H.365 Ligand excluded by PLIP SO4.94: 4 residues within 4Å: Chain H: Q.301, D.402, T.403, E.404 Ligand excluded by PLIP SO4.95: 4 residues within 4Å: Chain H: R.20 Chain L: L.3, S.35, A.37 Ligand excluded by PLIP SO4.96: 2 residues within 4Å: Chain H: R.302, K.400 Ligand excluded by PLIP SO4.97: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.98: 7 residues within 4Å: Chain H: G.107, E.108, Y.111, F.158, R.286, S.450 Ligands: SO4.102 Ligand excluded by PLIP SO4.99: 5 residues within 4Å: Chain D: G.46, V.47, R.48 Chain H: R.213, K.214 Ligand excluded by PLIP SO4.100: 8 residues within 4Å: Chain H: V.17, G.18, R.20, L.22, A.56 Chain L: Q.31, G.36, K.369 Ligand excluded by PLIP SO4.101: 2 residues within 4Å: Chain H: R.12, W.21 Ligand excluded by PLIP SO4.102: 8 residues within 4Å: Chain H: Y.111, F.158, R.165, R.286, V.293, S.450, F.456 Ligands: SO4.98 Ligand excluded by PLIP SO4.106: 4 residues within 4Å: Chain I: L.320, R.321, V.322, H.365 Ligand excluded by PLIP SO4.107: 4 residues within 4Å: Chain I: Q.301, D.402, T.403, E.404 Ligand excluded by PLIP SO4.108: 4 residues within 4Å: Chain G: L.3, S.35, A.37 Chain I: R.20 Ligand excluded by PLIP SO4.109: 2 residues within 4Å: Chain I: R.302, K.400 Ligand excluded by PLIP SO4.110: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.111: 7 residues within 4Å: Chain I: G.107, E.108, Y.111, F.158, R.286, S.450 Ligands: SO4.115 Ligand excluded by PLIP SO4.112: 5 residues within 4Å: Chain B: G.46, V.47, R.48 Chain I: R.213, K.214 Ligand excluded by PLIP SO4.113: 8 residues within 4Å: Chain G: Q.31, G.36, K.369 Chain I: V.17, G.18, R.20, L.22, A.56 Ligand excluded by PLIP SO4.114: 2 residues within 4Å: Chain I: R.12, W.21 Ligand excluded by PLIP SO4.115: 8 residues within 4Å: Chain I: Y.111, F.158, R.165, R.286, V.293, S.450, F.456 Ligands: SO4.111 Ligand excluded by PLIP SO4.119: 4 residues within 4Å: Chain J: L.320, R.321, V.322, H.365 Ligand excluded by PLIP SO4.120: 4 residues within 4Å: Chain J: Q.301, D.402, T.403, E.404 Ligand excluded by PLIP SO4.121: 4 residues within 4Å: Chain F: L.3, S.35, A.37 Chain J: R.20 Ligand excluded by PLIP SO4.122: 2 residues within 4Å: Chain J: R.302, K.400 Ligand excluded by PLIP SO4.123: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.124: 7 residues within 4Å: Chain J: G.107, E.108, Y.111, F.158, R.286, S.450 Ligands: SO4.128 Ligand excluded by PLIP SO4.125: 5 residues within 4Å: Chain J: R.213, K.214 Chain K: G.46, V.47, R.48 Ligand excluded by PLIP SO4.126: 8 residues within 4Å: Chain F: Q.31, G.36, K.369 Chain J: V.17, G.18, R.20, L.22, A.56 Ligand excluded by PLIP SO4.127: 2 residues within 4Å: Chain J: R.12, W.21 Ligand excluded by PLIP SO4.128: 8 residues within 4Å: Chain J: Y.111, F.158, R.165, R.286, V.293, S.450, F.456 Ligands: SO4.124 Ligand excluded by PLIP SO4.132: 4 residues within 4Å: Chain K: L.320, R.321, V.322, H.365 Ligand excluded by PLIP SO4.133: 4 residues within 4Å: Chain K: Q.301, D.402, T.403, E.404 Ligand excluded by PLIP SO4.134: 4 residues within 4Å: Chain J: L.3, S.35, A.37 Chain K: R.20 Ligand excluded by PLIP SO4.135: 2 residues within 4Å: Chain K: R.302, K.400 Ligand excluded by PLIP SO4.136: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.137: 7 residues within 4Å: Chain K: G.107, E.108, Y.111, F.158, R.286, S.450 Ligands: SO4.141 Ligand excluded by PLIP SO4.138: 5 residues within 4Å: Chain F: G.46, V.47, R.48 Chain K: R.213, K.214 Ligand excluded by PLIP SO4.139: 8 residues within 4Å: Chain J: Q.31, G.36, K.369 Chain K: V.17, G.18, R.20, L.22, A.56 Ligand excluded by PLIP SO4.140: 2 residues within 4Å: Chain K: R.12, W.21 Ligand excluded by PLIP SO4.141: 8 residues within 4Å: Chain K: Y.111, F.158, R.165, R.286, V.293, S.450, F.456 Ligands: SO4.137 Ligand excluded by PLIP SO4.145: 4 residues within 4Å: Chain L: L.320, R.321, V.322, H.365 Ligand excluded by PLIP SO4.146: 4 residues within 4Å: Chain L: Q.301, D.402, T.403, E.404 Ligand excluded by PLIP SO4.147: 4 residues within 4Å: Chain D: L.3, S.35, A.37 Chain L: R.20 Ligand excluded by PLIP SO4.148: 2 residues within 4Å: Chain L: R.302, K.400 Ligand excluded by PLIP SO4.149: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.150: 7 residues within 4Å: Chain L: G.107, E.108, Y.111, F.158, R.286, S.450 Ligands: SO4.154 Ligand excluded by PLIP SO4.151: 5 residues within 4Å: Chain H: G.46, V.47, R.48 Chain L: R.213, K.214 Ligand excluded by PLIP SO4.152: 8 residues within 4Å: Chain D: Q.31, G.36, K.369 Chain L: V.17, G.18, R.20, L.22, A.56 Ligand excluded by PLIP SO4.153: 2 residues within 4Å: Chain L: R.12, W.21 Ligand excluded by PLIP SO4.154: 8 residues within 4Å: Chain L: Y.111, F.158, R.165, R.286, V.293, S.450, F.456 Ligands: SO4.150 Ligand excluded by PLIP

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 2 residues within 4Å: Chain A: T.360, G.361 Ligand excluded by PLIP GOL.13: 4 residues within 4Å: Chain A: N.337, E.338, N.370 Chain E: R.55 Ligand excluded by PLIP GOL.25: 2 residues within 4Å: Chain B: T.360, G.361 Ligand excluded by PLIP GOL.26: 4 residues within 4Å: Chain B: N.337, E.338, N.370 Chain G: R.55 Ligand excluded by PLIP GOL.38: 2 residues within 4Å: Chain C: T.360, G.361 Ligand excluded by PLIP GOL.39: 4 residues within 4Å: Chain A: R.55 Chain C: N.337, E.338, N.370 Ligand excluded by PLIP GOL.51: 2 residues within 4Å: Chain D: T.360, G.361 Ligand excluded by PLIP GOL.52: 4 residues within 4Å: Chain D: N.337, E.338, N.370 Chain L: R.55 Ligand excluded by PLIP GOL.64: 2 residues within 4Å: Chain E: T.360, G.361 Ligand excluded by PLIP GOL.65: 4 residues within 4Å: Chain C: R.55 Chain E: N.337, E.338, N.370 Ligand excluded by PLIP GOL.77: 2 residues within 4Å: Chain F: T.360, G.361 Ligand excluded by PLIP GOL.78: 4 residues within 4Å: Chain F: N.337, E.338, N.370 Chain J: R.55 Ligand excluded by PLIP GOL.90: 2 residues within 4Å: Chain G: T.360, G.361 Ligand excluded by PLIP GOL.91: 4 residues within 4Å: Chain G: N.337, E.338, N.370 Chain I: R.55 Ligand excluded by PLIP GOL.103: 2 residues within 4Å: Chain H: T.360, G.361 Ligand excluded by PLIP GOL.104: 4 residues within 4Å: Chain D: R.55 Chain H: N.337, E.338, N.370 Ligand excluded by PLIP GOL.116: 2 residues within 4Å: Chain I: T.360, G.361 Ligand excluded by PLIP GOL.117: 4 residues within 4Å: Chain B: R.55 Chain I: N.337, E.338, N.370 Ligand excluded by PLIP GOL.129: 2 residues within 4Å: Chain J: T.360, G.361 Ligand excluded by PLIP GOL.130: 4 residues within 4Å: Chain J: N.337, E.338, N.370 Chain K: R.55 Ligand excluded by PLIP GOL.142: 2 residues within 4Å: Chain K: T.360, G.361 Ligand excluded by PLIP GOL.143: 4 residues within 4Å: Chain F: R.55 Chain K: N.337, E.338, N.370 Ligand excluded by PLIP GOL.155: 2 residues within 4Å: Chain L: T.360, G.361 Ligand excluded by PLIP GOL.156: 4 residues within 4Å: Chain H: R.55 Chain L: N.337, E.338, N.370 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y.-G. et al., Redox-Switch Modulation of Human Ssadh by Dynamic Catalytic Loop. Embo J. (2009)

Release Date

2009-06-09

Peptides

SUCCINATE-SEMIALDEHYDE DEHYDROGENASE, MITOCHONDRIAL: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

L
A

SUCCINATE-SEMIALDEHYDE DEHYDROGENASE, MITOCHONDRIAL

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