SMTL ID : 2w8q.1 (2 other biounits)

The crystal structure of human SSADH in complex with SSA.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-12-mer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: L.320, R.321, V.322, H.365 Ligand excluded by PLIP SO4.2: 3 residues within 4Å: Chain A: Q.301, T.403, E.404 Ligand excluded by PLIP SO4.3: 3 residues within 4Å: Chain A: F.234, S.237, T.240 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: R.20 Chain C: 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: SIN.12 Ligand excluded by PLIP SO4.8: 6 residues within 4Å: Chain A: R.213, K.214 Chain E: G.46, V.47, R.48, E.49 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain A: G.19, R.20, W.21 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain B: L.320, R.321, V.322, H.365 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain B: Q.301, T.403, E.404 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain B: F.234, S.237, T.240 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain B: R.20 Chain I: S.35, A.37 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain B: R.302, K.400 Ligand excluded by PLIP SO4.18: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.19: 7 residues within 4Å: Chain B: G.107, E.108, Y.111, F.158, R.286, S.450 Ligands: SIN.24 Ligand excluded by PLIP SO4.20: 6 residues within 4Å: Chain B: R.213, K.214 Chain G: G.46, V.47, R.48, E.49 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain B: G.19, R.20, W.21 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain C: L.320, R.321, V.322, H.365 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain C: Q.301, T.403, E.404 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain C: F.234, S.237, T.240 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain C: R.20 Chain E: S.35, A.37 Ligand excluded by PLIP SO4.29: 2 residues within 4Å: Chain C: R.302, K.400 Ligand excluded by PLIP SO4.30: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.31: 7 residues within 4Å: Chain C: G.107, E.108, Y.111, F.158, R.286, S.450 Ligands: SIN.36 Ligand excluded by PLIP SO4.32: 6 residues within 4Å: Chain A: G.46, V.47, R.48, E.49 Chain C: R.213, K.214 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain C: G.19, R.20, W.21 Ligand excluded by PLIP SO4.37: 4 residues within 4Å: Chain D: L.320, R.321, V.322, H.365 Ligand excluded by PLIP SO4.38: 3 residues within 4Å: Chain D: Q.301, T.403, E.404 Ligand excluded by PLIP SO4.39: 3 residues within 4Å: Chain D: F.234, S.237, T.240 Ligand excluded by PLIP SO4.40: 3 residues within 4Å: Chain D: R.20 Chain H: S.35, A.37 Ligand excluded by PLIP SO4.41: 2 residues within 4Å: Chain D: R.302, K.400 Ligand excluded by PLIP SO4.42: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.43: 7 residues within 4Å: Chain D: G.107, E.108, Y.111, F.158, R.286, S.450 Ligands: SIN.48 Ligand excluded by PLIP SO4.44: 6 residues within 4Å: Chain D: R.213, K.214 Chain L: G.46, V.47, R.48, E.49 Ligand excluded by PLIP SO4.45: 3 residues within 4Å: Chain D: G.19, R.20, W.21 Ligand excluded by PLIP SO4.49: 4 residues within 4Å: Chain E: L.320, R.321, V.322, H.365 Ligand excluded by PLIP SO4.50: 3 residues within 4Å: Chain E: Q.301, T.403, E.404 Ligand excluded by PLIP SO4.51: 3 residues within 4Å: Chain E: F.234, S.237, T.240 Ligand excluded by PLIP SO4.52: 3 residues within 4Å: Chain A: S.35, A.37 Chain E: R.20 Ligand excluded by PLIP SO4.53: 2 residues within 4Å: Chain E: R.302, K.400 Ligand excluded by PLIP SO4.54: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.55: 7 residues within 4Å: Chain E: G.107, E.108, Y.111, F.158, R.286, S.450 Ligands: SIN.60 Ligand excluded by PLIP SO4.56: 6 residues within 4Å: Chain C: G.46, V.47, R.48, E.49 Chain E: R.213, K.214 Ligand excluded by PLIP SO4.57: 3 residues within 4Å: Chain E: G.19, R.20, W.21 Ligand excluded by PLIP SO4.61: 4 residues within 4Å: Chain F: L.320, R.321, V.322, H.365 Ligand excluded by PLIP SO4.62: 3 residues within 4Å: Chain F: Q.301, T.403, E.404 Ligand excluded by PLIP SO4.63: 3 residues within 4Å: Chain F: F.234, S.237, T.240 Ligand excluded by PLIP SO4.64: 3 residues within 4Å: Chain F: R.20 Chain K: S.35, A.37 Ligand excluded by PLIP SO4.65: 2 residues within 4Å: Chain F: R.302, K.400 Ligand excluded by PLIP SO4.66: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.67: 7 residues within 4Å: Chain F: G.107, E.108, Y.111, F.158, R.286, S.450 Ligands: SIN.72 Ligand excluded by PLIP SO4.68: 6 residues within 4Å: Chain F: R.213, K.214 Chain J: G.46, V.47, R.48, E.49 Ligand excluded by PLIP SO4.69: 3 residues within 4Å: Chain F: G.19, R.20, W.21 Ligand excluded by PLIP SO4.73: 4 residues within 4Å: Chain G: L.320, R.321, V.322, H.365 Ligand excluded by PLIP SO4.74: 3 residues within 4Å: Chain G: Q.301, T.403, E.404 Ligand excluded by PLIP SO4.75: 3 residues within 4Å: Chain G: F.234, S.237, T.240 Ligand excluded by PLIP SO4.76: 3 residues within 4Å: Chain B: S.35, A.37 Chain G: R.20 Ligand excluded by PLIP SO4.77: 2 residues within 4Å: Chain G: R.302, K.400 Ligand excluded by PLIP SO4.78: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.79: 7 residues within 4Å: Chain G: G.107, E.108, Y.111, F.158, R.286, S.450 Ligands: SIN.84 Ligand excluded by PLIP SO4.80: 6 residues within 4Å: Chain G: R.213, K.214 Chain I: G.46, V.47, R.48, E.49 Ligand excluded by PLIP SO4.81: 3 residues within 4Å: Chain G: G.19, R.20, W.21 Ligand excluded by PLIP SO4.85: 4 residues within 4Å: Chain H: L.320, R.321, V.322, H.365 Ligand excluded by PLIP SO4.86: 3 residues within 4Å: Chain H: Q.301, T.403, E.404 Ligand excluded by PLIP SO4.87: 3 residues within 4Å: Chain H: F.234, S.237, T.240 Ligand excluded by PLIP SO4.88: 3 residues within 4Å: Chain H: R.20 Chain L: S.35, A.37 Ligand excluded by PLIP SO4.89: 2 residues within 4Å: Chain H: R.302, K.400 Ligand excluded by PLIP SO4.90: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.91: 7 residues within 4Å: Chain H: G.107, E.108, Y.111, F.158, R.286, S.450 Ligands: SIN.96 Ligand excluded by PLIP SO4.92: 6 residues within 4Å: Chain D: G.46, V.47, R.48, E.49 Chain H: R.213, K.214 Ligand excluded by PLIP SO4.93: 3 residues within 4Å: Chain H: G.19, R.20, W.21 Ligand excluded by PLIP SO4.97: 4 residues within 4Å: Chain I: L.320, R.321, V.322, H.365 Ligand excluded by PLIP SO4.98: 3 residues within 4Å: Chain I: Q.301, T.403, E.404 Ligand excluded by PLIP SO4.99: 3 residues within 4Å: Chain I: F.234, S.237, T.240 Ligand excluded by PLIP SO4.100: 3 residues within 4Å: Chain G: S.35, A.37 Chain I: R.20 Ligand excluded by PLIP SO4.101: 2 residues within 4Å: Chain I: R.302, K.400 Ligand excluded by PLIP SO4.102: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.103: 7 residues within 4Å: Chain I: G.107, E.108, Y.111, F.158, R.286, S.450 Ligands: SIN.108 Ligand excluded by PLIP SO4.104: 6 residues within 4Å: Chain B: G.46, V.47, R.48, E.49 Chain I: R.213, K.214 Ligand excluded by PLIP SO4.105: 3 residues within 4Å: Chain I: G.19, R.20, W.21 Ligand excluded by PLIP SO4.109: 4 residues within 4Å: Chain J: L.320, R.321, V.322, H.365 Ligand excluded by PLIP SO4.110: 3 residues within 4Å: Chain J: Q.301, T.403, E.404 Ligand excluded by PLIP SO4.111: 3 residues within 4Å: Chain J: F.234, S.237, T.240 Ligand excluded by PLIP SO4.112: 3 residues within 4Å: Chain F: S.35, A.37 Chain J: R.20 Ligand excluded by PLIP SO4.113: 2 residues within 4Å: Chain J: R.302, K.400 Ligand excluded by PLIP SO4.114: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.115: 7 residues within 4Å: Chain J: G.107, E.108, Y.111, F.158, R.286, S.450 Ligands: SIN.120 Ligand excluded by PLIP SO4.116: 6 residues within 4Å: Chain J: R.213, K.214 Chain K: G.46, V.47, R.48, E.49 Ligand excluded by PLIP SO4.117: 3 residues within 4Å: Chain J: G.19, R.20, W.21 Ligand excluded by PLIP SO4.121: 4 residues within 4Å: Chain K: L.320, R.321, V.322, H.365 Ligand excluded by PLIP SO4.122: 3 residues within 4Å: Chain K: Q.301, T.403, E.404 Ligand excluded by PLIP SO4.123: 3 residues within 4Å: Chain K: F.234, S.237, T.240 Ligand excluded by PLIP SO4.124: 3 residues within 4Å: Chain J: S.35, A.37 Chain K: R.20 Ligand excluded by PLIP SO4.125: 2 residues within 4Å: Chain K: R.302, K.400 Ligand excluded by PLIP SO4.126: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.127: 7 residues within 4Å: Chain K: G.107, E.108, Y.111, F.158, R.286, S.450 Ligands: SIN.132 Ligand excluded by PLIP SO4.128: 6 residues within 4Å: Chain F: G.46, V.47, R.48, E.49 Chain K: R.213, K.214 Ligand excluded by PLIP SO4.129: 3 residues within 4Å: Chain K: G.19, R.20, W.21 Ligand excluded by PLIP SO4.133: 4 residues within 4Å: Chain L: L.320, R.321, V.322, H.365 Ligand excluded by PLIP SO4.134: 3 residues within 4Å: Chain L: Q.301, T.403, E.404 Ligand excluded by PLIP SO4.135: 3 residues within 4Å: Chain L: F.234, S.237, T.240 Ligand excluded by PLIP SO4.136: 3 residues within 4Å: Chain D: S.35, A.37 Chain L: R.20 Ligand excluded by PLIP SO4.137: 2 residues within 4Å: Chain L: R.302, K.400 Ligand excluded by PLIP SO4.138: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.139: 7 residues within 4Å: Chain L: G.107, E.108, Y.111, F.158, R.286, S.450 Ligands: SIN.144 Ligand excluded by PLIP SO4.140: 6 residues within 4Å: Chain H: G.46, V.47, R.48, E.49 Chain L: R.213, K.214 Ligand excluded by PLIP SO4.141: 3 residues within 4Å: Chain L: G.19, R.20, W.21 Ligand excluded by PLIP

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 3 residues within 4Å: Chain A: T.360, G.361, K.363 Ligand excluded by PLIP GOL.11: 3 residues within 4Å: Chain A: N.337, E.338 Chain E: R.55 Ligand excluded by PLIP GOL.22: 3 residues within 4Å: Chain B: T.360, G.361, K.363 Ligand excluded by PLIP GOL.23: 3 residues within 4Å: Chain B: N.337, E.338 Chain G: R.55 Ligand excluded by PLIP GOL.34: 3 residues within 4Å: Chain C: T.360, G.361, K.363 Ligand excluded by PLIP GOL.35: 3 residues within 4Å: Chain A: R.55 Chain C: N.337, E.338 Ligand excluded by PLIP GOL.46: 3 residues within 4Å: Chain D: T.360, G.361, K.363 Ligand excluded by PLIP GOL.47: 3 residues within 4Å: Chain D: N.337, E.338 Chain L: R.55 Ligand excluded by PLIP GOL.58: 3 residues within 4Å: Chain E: T.360, G.361, K.363 Ligand excluded by PLIP GOL.59: 3 residues within 4Å: Chain C: R.55 Chain E: N.337, E.338 Ligand excluded by PLIP GOL.70: 3 residues within 4Å: Chain F: T.360, G.361, K.363 Ligand excluded by PLIP GOL.71: 3 residues within 4Å: Chain F: N.337, E.338 Chain J: R.55 Ligand excluded by PLIP GOL.82: 3 residues within 4Å: Chain G: T.360, G.361, K.363 Ligand excluded by PLIP GOL.83: 3 residues within 4Å: Chain G: N.337, E.338 Chain I: R.55 Ligand excluded by PLIP GOL.94: 3 residues within 4Å: Chain H: T.360, G.361, K.363 Ligand excluded by PLIP GOL.95: 3 residues within 4Å: Chain D: R.55 Chain H: N.337, E.338 Ligand excluded by PLIP GOL.106: 3 residues within 4Å: Chain I: T.360, G.361, K.363 Ligand excluded by PLIP GOL.107: 3 residues within 4Å: Chain B: R.55 Chain I: N.337, E.338 Ligand excluded by PLIP GOL.118: 3 residues within 4Å: Chain J: T.360, G.361, K.363 Ligand excluded by PLIP GOL.119: 3 residues within 4Å: Chain J: N.337, E.338 Chain K: R.55 Ligand excluded by PLIP GOL.130: 3 residues within 4Å: Chain K: T.360, G.361, K.363 Ligand excluded by PLIP GOL.131: 3 residues within 4Å: Chain F: R.55 Chain K: N.337, E.338 Ligand excluded by PLIP GOL.142: 3 residues within 4Å: Chain L: T.360, G.361, K.363 Ligand excluded by PLIP GOL.143: 3 residues within 4Å: Chain H: R.55 Chain L: N.337, E.338 Ligand excluded by PLIP

12 x SIN: SUCCINIC ACID(Non-covalent)

SIN.12: 10 residues within 4Å: Chain A: Y.111, F.158, R.165, E.258, R.286, A.292, V.293, S.450, F.456 Ligands: SO4.7 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.158, A:V.293 Hydrogen bonds: A:A.292, A:V.293, A:S.450 Salt bridges: A:R.165, A:R.286 SIN.24: 10 residues within 4Å: Chain B: Y.111, F.158, R.165, E.258, R.286, A.292, V.293, S.450, F.456 Ligands: SO4.19 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.158, B:V.293 Hydrogen bonds: B:A.292, B:V.293, B:S.450 Salt bridges: B:R.165, B:R.286 SIN.36: 10 residues within 4Å: Chain C: Y.111, F.158, R.165, E.258, R.286, A.292, V.293, S.450, F.456 Ligands: SO4.31 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.158, C:V.293 Hydrogen bonds: C:A.292, C:V.293, C:S.450 Salt bridges: C:R.165, C:R.286 SIN.48: 10 residues within 4Å: Chain D: Y.111, F.158, R.165, E.258, R.286, A.292, V.293, S.450, F.456 Ligands: SO4.43 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:F.158, D:V.293 Hydrogen bonds: D:A.292, D:V.293, D:S.450 Salt bridges: D:R.165, D:R.286 SIN.60: 10 residues within 4Å: Chain E: Y.111, F.158, R.165, E.258, R.286, A.292, V.293, S.450, F.456 Ligands: SO4.55 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:F.158, E:V.293 Hydrogen bonds: E:A.292, E:V.293, E:S.450 Salt bridges: E:R.165, E:R.286 SIN.72: 10 residues within 4Å: Chain F: Y.111, F.158, R.165, E.258, R.286, A.292, V.293, S.450, F.456 Ligands: SO4.67 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:F.158, F:V.293 Hydrogen bonds: F:A.292, F:V.293, F:S.450 Salt bridges: F:R.165, F:R.286 SIN.84: 10 residues within 4Å: Chain G: Y.111, F.158, R.165, E.258, R.286, A.292, V.293, S.450, F.456 Ligands: SO4.79 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:F.158, G:V.293 Hydrogen bonds: G:A.292, G:V.293, G:S.450 Salt bridges: G:R.165, G:R.286 SIN.96: 10 residues within 4Å: Chain H: Y.111, F.158, R.165, E.258, R.286, A.292, V.293, S.450, F.456 Ligands: SO4.91 7 PLIP interactions: 7 interactions with chain H Hydrophobic interactions: H:F.158, H:V.293 Hydrogen bonds: H:A.292, H:V.293, H:S.450 Salt bridges: H:R.165, H:R.286 SIN.108: 10 residues within 4Å: Chain I: Y.111, F.158, R.165, E.258, R.286, A.292, V.293, S.450, F.456 Ligands: SO4.103 7 PLIP interactions: 7 interactions with chain I Hydrophobic interactions: I:F.158, I:V.293 Hydrogen bonds: I:A.292, I:V.293, I:S.450 Salt bridges: I:R.165, I:R.286 SIN.120: 10 residues within 4Å: Chain J: Y.111, F.158, R.165, E.258, R.286, A.292, V.293, S.450, F.456 Ligands: SO4.115 7 PLIP interactions: 7 interactions with chain J Hydrophobic interactions: J:F.158, J:V.293 Hydrogen bonds: J:A.292, J:V.293, J:S.450 Salt bridges: J:R.165, J:R.286 SIN.132: 10 residues within 4Å: Chain K: Y.111, F.158, R.165, E.258, R.286, A.292, V.293, S.450, F.456 Ligands: SO4.127 7 PLIP interactions: 7 interactions with chain K Hydrophobic interactions: K:F.158, K:V.293 Hydrogen bonds: K:A.292, K:V.293, K:S.450 Salt bridges: K:R.165, K:R.286 SIN.144: 10 residues within 4Å: Chain L: Y.111, F.158, R.165, E.258, R.286, A.292, V.293, S.450, F.456 Ligands: SO4.139 7 PLIP interactions: 7 interactions with chain L Hydrophobic interactions: L:F.158, L:V.293 Hydrogen bonds: L:A.292, L:V.293, L:S.450 Salt bridges: L:R.165, L:R.286

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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