SMTL ID : 2w8r.2 (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-tetramer

Ligands

4 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 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.154, B:K.180, B:E.183, B:S.237 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 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.154, C:K.180, C:E.183, C:S.237, C:T.240 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 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.154, D:K.180, D:E.183, D:S.237, D:T.240

40 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: 1 residues within 4Å: Chain A: R.20 Ligand excluded by PLIP SO4.5: 2 residues within 4Å: Chain A: R.302, K.400 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain B: Y.127, K.470 Ligands: SO4.19 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: 2 residues within 4Å: Chain A: R.213, K.214 Ligand excluded by PLIP SO4.9: 5 residues within 4Å: Chain A: V.17, G.18, R.20, L.22, A.56 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: 1 residues within 4Å: Chain B: R.20 Ligand excluded by PLIP SO4.18: 2 residues within 4Å: Chain B: R.302, K.400 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain A: Y.127, K.470 Ligands: SO4.6 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: 2 residues within 4Å: Chain B: R.213, K.214 Ligand excluded by PLIP SO4.22: 5 residues within 4Å: Chain B: V.17, G.18, R.20, L.22, A.56 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: 1 residues within 4Å: Chain C: R.20 Ligand excluded by PLIP SO4.31: 2 residues within 4Å: Chain C: R.302, K.400 Ligand excluded by PLIP SO4.32: 3 residues within 4Å: Chain D: Y.127, K.470 Ligands: SO4.45 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: 2 residues within 4Å: Chain C: R.213, K.214 Ligand excluded by PLIP SO4.35: 5 residues within 4Å: Chain C: V.17, G.18, R.20, L.22, A.56 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: 1 residues within 4Å: Chain D: R.20 Ligand excluded by PLIP SO4.44: 2 residues within 4Å: Chain D: R.302, K.400 Ligand excluded by PLIP SO4.45: 3 residues within 4Å: Chain C: Y.127, K.470 Ligands: SO4.32 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: 2 residues within 4Å: Chain D: R.213, K.214 Ligand excluded by PLIP SO4.48: 5 residues within 4Å: Chain D: V.17, G.18, R.20, L.22, A.56 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

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 2 residues within 4Å: Chain A: T.360, G.361 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.360, A:G.361, A:G.361 GOL.13: 3 residues within 4Å: Chain A: N.337, E.338, N.370 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.338, A:N.370 GOL.25: 2 residues within 4Å: Chain B: T.360, G.361 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.361, B:G.361 GOL.26: 3 residues within 4Å: Chain B: N.337, E.338, N.370 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.338, B:N.370 GOL.38: 2 residues within 4Å: Chain C: T.360, G.361 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.361, C:G.361 GOL.39: 3 residues within 4Å: Chain C: N.337, E.338, N.370 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.338, C:N.370 GOL.51: 2 residues within 4Å: Chain D: T.360, G.361 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.360, D:G.361, D:G.361 GOL.52: 3 residues within 4Å: Chain D: N.337, E.338, N.370 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.338, D:N.370

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

SUCCINATE-SEMIALDEHYDE DEHYDROGENASE, MITOCHONDRIAL

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