SMTL ID : 1mx3.3 (2 other biounits)

Crystal structure of CtBP dehydrogenase core holo form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 28 residues within 4Å: Chain A: S.94, G.95, T.122, I.174, G.175, L.176, G.177, R.178, V.179, Y.197, D.198, P.199, Y.200, L.201, H.230, C.231, G.232, N.234, N.237, T.258, A.259, R.260, D.284, V.285, H.309, A.311, W.312 Ligands: ACY.2 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:W.312 Hydrogen bonds: A:S.94, A:L.176, A:R.178, A:V.179, A:C.231, A:G.232, A:L.233, A:N.237, A:D.284, A:D.284, A:W.312 Water bridges: A:S.94, A:D.97, A:D.97, A:G.177, A:R.178, A:R.178, A:G.180, A:Y.197, A:N.234, A:N.234, A:R.260 Salt bridges: A:R.178 pi-Stacking: A:Y.200 NAD.3: 28 residues within 4Å: Chain B: S.94, G.95, T.122, I.174, G.175, L.176, G.177, R.178, V.179, Y.197, D.198, P.199, Y.200, L.201, H.230, C.231, G.232, N.234, N.237, T.258, A.259, R.260, D.284, V.285, H.309, A.311, W.312 Ligands: ACY.4 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:W.312 Hydrogen bonds: B:S.94, B:L.176, B:R.178, B:V.179, B:C.231, B:G.232, B:L.233, B:N.237, B:D.284, B:D.284, B:W.312 Water bridges: B:S.94, B:D.97, B:D.97, B:G.177, B:R.178, B:R.178, B:G.180, B:Y.197, B:N.234, B:N.234, B:R.260 Salt bridges: B:R.178 pi-Stacking: B:Y.200 NAD.5: 28 residues within 4Å: Chain C: S.94, G.95, T.122, I.174, G.175, L.176, G.177, R.178, V.179, Y.197, D.198, P.199, Y.200, L.201, H.230, C.231, G.232, N.234, N.237, T.258, A.259, R.260, D.284, V.285, H.309, A.311, W.312 Ligands: ACY.6 26 PLIP interactions: 26 interactions with chain C Hydrophobic interactions: C:W.312 Hydrogen bonds: C:S.94, C:L.176, C:R.178, C:V.179, C:C.231, C:G.232, C:L.233, C:N.237, C:D.284, C:W.312 Water bridges: C:S.94, C:D.97, C:G.177, C:R.178, C:R.178, C:G.180, C:Y.197, C:Y.197, C:Y.200, C:Y.200, C:N.234, C:R.260, C:R.260 Salt bridges: C:R.178 pi-Stacking: C:Y.200 NAD.7: 28 residues within 4Å: Chain D: S.94, G.95, T.122, I.174, G.175, L.176, G.177, R.178, V.179, Y.197, D.198, P.199, Y.200, L.201, H.230, C.231, G.232, N.234, N.237, T.258, A.259, R.260, D.284, V.285, H.309, A.311, W.312 Ligands: ACY.8 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:W.312 Hydrogen bonds: D:S.94, D:L.176, D:R.178, D:V.179, D:C.231, D:G.232, D:L.233, D:N.237, D:D.284, D:W.312 Water bridges: D:S.94, D:D.97, D:G.177, D:R.178, D:R.178, D:G.180, D:Y.197, D:Y.197, D:Y.200, D:Y.200, D:N.234, D:R.260, D:R.260 Salt bridges: D:R.178 pi-Stacking: D:Y.200

4 x ACY: ACETIC ACID(Non-functional Binders)

ACY.2: 8 residues within 4Å: Chain A: R.91, G.93, S.94, G.95, R.260, H.309, W.312 Ligands: NAD.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.312 Hydrogen bonds: A:S.94, A:G.95 Water bridges: A:H.71, A:H.71, A:R.260 Salt bridges: A:H.71, A:R.91, A:R.260, A:H.309 ACY.4: 8 residues within 4Å: Chain B: R.91, G.93, S.94, G.95, R.260, H.309, W.312 Ligands: NAD.3 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.312 Hydrogen bonds: B:S.94, B:G.95 Water bridges: B:H.71, B:H.71, B:R.260 Salt bridges: B:H.71, B:R.91, B:R.260, B:H.309 ACY.6: 8 residues within 4Å: Chain C: R.91, G.93, S.94, G.95, R.260, H.309, W.312 Ligands: NAD.5 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:W.312 Hydrogen bonds: C:S.94, C:G.95 Water bridges: C:H.71, C:H.71, C:R.91, C:R.260 Salt bridges: C:H.71, C:R.91, C:R.260, C:H.309 ACY.8: 8 residues within 4Å: Chain D: R.91, G.93, S.94, G.95, R.260, H.309, W.312 Ligands: NAD.7 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:W.312 Hydrogen bonds: D:S.94, D:G.95 Water bridges: D:H.71, D:H.71, D:R.91, D:R.260 Salt bridges: D:H.71, D:R.91, D:R.260, D:H.309

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, V. et al., Transcription Corepressor CtBP Is an NAD+-Regulated Dehydrogenase. Mol.Cell (2002)

Release Date

2002-12-18

Peptides

C-terminal binding protein 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

C-terminal binding protein 1

Related Entries With Identical Sequence