SMTL ID : 1pt9.3 (5 other biounits)

Crystal Structure Analysis of the DIII Component of Transhydrogenase with a Thio-Nicotinamide Nucleotide Analogue

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: R.164 Chain C: V.168 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Water bridges: C:V.168 Salt bridges: A:R.164 SO4.4: 2 residues within 4Å: Chain B: R.164 Chain D: V.168 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B Water bridges: D:V.168, B:R.164 Salt bridges: B:R.164 SO4.7: 1 residues within 4Å: Chain C: R.164 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.164, C:R.164 Salt bridges: C:R.164 SO4.10: 1 residues within 4Å: Chain D: R.164 3 PLIP interactions: 3 interactions with chain D Water bridges: D:R.164, D:R.164 Salt bridges: D:R.164

4 x TAP: 7-THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

TAP.2: 30 residues within 4Å: Chain A: G.53, Y.54, G.55, A.59, V.86, A.87, G.88, R.89, M.90, P.91, G.128, A.129, N.130, D.131, T.132, K.163, R.164, S.165, G.167, V.168, G.169, Y.170, G.188, D.189, A.190 Chain B: A.146, G.147, M.148, P.149 Ligands: GOL.3 30 PLIP interactions: 29 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:V.86 Hydrogen bonds: A:Y.54, A:G.55, A:G.88, A:G.88, A:R.89, A:N.130, A:N.130, A:D.131, A:D.131, A:D.131, A:T.132, A:K.163, A:R.164, A:S.165, A:S.165, A:G.167, A:Y.170, A:D.189, A:A.190 Water bridges: A:R.89, A:R.164, A:R.164, A:S.165, C:V.168 Salt bridges: A:R.89, A:K.163, A:R.164 pi-Stacking: A:Y.170 pi-Cation interactions: A:R.164 TAP.5: 30 residues within 4Å: Chain A: A.146, G.147, M.148, P.149 Chain B: G.53, Y.54, G.55, A.59, V.86, A.87, G.88, R.89, M.90, P.91, G.128, A.129, N.130, D.131, T.132, K.163, R.164, S.165, G.167, V.168, G.169, Y.170, G.188, D.189, A.190 Ligands: GOL.6 30 PLIP interactions: 29 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:V.86 Hydrogen bonds: B:Y.54, B:G.55, B:G.88, B:G.88, B:R.89, B:N.130, B:N.130, B:D.131, B:D.131, B:T.132, B:K.163, B:R.164, B:S.165, B:S.165, B:G.167, B:Y.170, B:D.189, B:A.190 Water bridges: B:R.89, B:R.164, B:R.164, B:R.164, B:S.165, D:V.168 Salt bridges: B:R.89, B:K.163, B:R.164 pi-Stacking: B:Y.170 pi-Cation interactions: B:R.164 TAP.8: 26 residues within 4Å: Chain C: G.53, Y.54, G.55, A.58, A.59, V.86, A.87, G.88, R.89, M.90, P.91, G.128, A.129, N.130, D.131, T.132, K.163, R.164, S.165, V.168, G.169, Y.170, G.188, D.189, A.190 Ligands: GOL.9 28 PLIP interactions: 28 interactions with chain C Hydrogen bonds: C:Y.54, C:G.55, C:G.88, C:G.88, C:R.89, C:N.130, C:N.130, C:D.131, C:D.131, C:D.131, C:T.132, C:R.164, C:S.165, C:S.165, C:Y.170, C:A.171, C:D.189, C:A.190 Water bridges: C:R.164, C:S.165, C:S.165, C:S.165, C:S.165, C:V.168 Salt bridges: C:K.163, C:R.164 pi-Stacking: C:Y.170 pi-Cation interactions: C:R.164 TAP.11: 26 residues within 4Å: Chain D: G.53, Y.54, G.55, A.58, A.59, V.86, A.87, G.88, R.89, M.90, P.91, G.128, A.129, N.130, D.131, T.132, K.163, R.164, S.165, V.168, G.169, Y.170, G.188, D.189, A.190 Ligands: GOL.12 27 PLIP interactions: 27 interactions with chain D Hydrogen bonds: D:Y.54, D:G.55, D:G.88, D:G.88, D:R.89, D:N.130, D:N.130, D:D.131, D:D.131, D:T.132, D:R.164, D:S.165, D:S.165, D:Y.170, D:A.171, D:D.189, D:A.190 Water bridges: D:R.164, D:S.165, D:S.165, D:S.165, D:S.165, D:V.168 Salt bridges: D:K.163, D:R.164 pi-Stacking: D:Y.170 pi-Cation interactions: D:R.164

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: H.84, V.86, D.131, I.145, M.148, P.149, V.150 Ligands: TAP.2 No protein-ligand interaction detected (PLIP) GOL.6: 8 residues within 4Å: Chain B: H.84, V.86, D.131, I.145, M.148, P.149, V.150 Ligands: TAP.5 No protein-ligand interaction detected (PLIP) GOL.9: 8 residues within 4Å: Chain C: H.84, V.86, D.131, I.145, M.148, P.149, V.150 Ligands: TAP.8 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.84 GOL.12: 8 residues within 4Å: Chain D: H.84, V.86, D.131, I.145, M.148, P.149, V.150 Ligands: TAP.11 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, A. et al., Interactions between transhydrogenase and thio-nicotinamide analogues of NAD(H) and NADP(H) underline the importance of nucleotide conformational changes in coupling to proton translocation. J.Biol.Chem. (2003)

Release Date

2003-10-07

Peptides

NAD(P) transhydrogenase, mitochondrial: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
B

D
B

NAD(P) transhydrogenase, mitochondrial

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