SMTL ID : 4u6s.2 (1 other biounit)

CtBP1 in complex with substrate phenylpyruvate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 30 residues within 4Å: Chain A: S.94, G.95, P.115, 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, L.240, T.258, A.259, R.260, D.284, V.285, H.309, A.311, W.312 Ligands: PPY.2 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:T.122, A:W.312 Hydrogen bonds: A:L.176, A:R.178, A:V.179, A:C.231, A:G.232, A:N.234, A:N.237, A:T.258, A:D.284, A:A.311, A:W.312 Water bridges: A:S.94, A:S.94, A:D.97, A:G.177, A:R.178, A:G.180, A:Y.197, A:L.233 Salt bridges: A:R.178 pi-Stacking: A:Y.200 NAD.5: 30 residues within 4Å: Chain B: S.94, G.95, P.115, 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, L.240, T.258, A.259, R.260, D.284, V.285, H.309, A.311, W.312 Ligands: PPY.6 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:T.122, B:W.312 Hydrogen bonds: B:L.176, B:R.178, B:V.179, B:C.231, B:G.232, B:N.234, B:N.237, B:T.258, B:D.284, B:A.311, B:W.312 Water bridges: B:S.94, B:S.94, B:D.97, B:G.177, B:R.178, B:G.180, B:Y.197, B:L.233 Salt bridges: B:R.178 pi-Stacking: B:Y.200 NAD.9: 30 residues within 4Å: Chain C: S.94, G.95, P.115, 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, L.240, T.258, A.259, R.260, D.284, V.285, H.309, A.311, W.312 Ligands: PPY.10 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:T.122, C:W.312 Hydrogen bonds: C:L.176, C:R.178, C:V.179, C:C.231, C:G.232, C:N.234, C:N.237, C:T.258, C:A.311, C:W.312 Water bridges: C:S.94, C:S.94, C:D.97, C:G.177, C:R.178, C:G.180, C:Y.197, C:Y.197, C:L.233 Salt bridges: C:R.178 pi-Stacking: C:Y.200 NAD.13: 30 residues within 4Å: Chain D: S.94, G.95, P.115, 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, L.240, T.258, A.259, R.260, D.284, V.285, H.309, A.311, W.312 Ligands: PPY.14 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:T.122, D:W.312 Hydrogen bonds: D:L.176, D:R.178, D:V.179, D:C.231, D:G.232, D:N.234, D:N.237, D:T.258, D:A.311, D:W.312 Water bridges: D:S.94, D:S.94, D:D.97, D:G.177, D:R.178, D:G.180, D:Y.197, D:Y.197, D:L.233 Salt bridges: D:R.178 pi-Stacking: D:Y.200

4 x PPY: 3-PHENYLPYRUVIC ACID(Non-covalent)

PPY.2: 13 residues within 4Å: Chain A: Y.70, H.71, R.91, I.92, G.93, S.94, G.95, A.117, R.260, H.309, W.312, M.321 Ligands: NAD.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.70, A:W.312 Hydrogen bonds: A:S.94, A:G.95 Salt bridges: A:R.91, A:R.260, A:H.309 pi-Stacking: A:W.312, A:W.312 pi-Cation interactions: A:R.91 PPY.6: 13 residues within 4Å: Chain B: Y.70, H.71, R.91, I.92, G.93, S.94, G.95, A.117, R.260, H.309, W.312, M.321 Ligands: NAD.5 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.70, B:W.312 Hydrogen bonds: B:S.94, B:G.95 Salt bridges: B:R.91, B:R.260, B:H.309 pi-Stacking: B:W.312, B:W.312 pi-Cation interactions: B:R.91 PPY.10: 13 residues within 4Å: Chain C: Y.70, H.71, R.91, I.92, G.93, S.94, G.95, A.117, R.260, H.309, W.312, M.321 Ligands: NAD.9 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:Y.70, C:W.312 Hydrogen bonds: C:S.94, C:G.95 Salt bridges: C:R.91, C:R.260, C:H.309 pi-Stacking: C:W.312, C:W.312 pi-Cation interactions: C:R.91 PPY.14: 13 residues within 4Å: Chain D: Y.70, H.71, R.91, I.92, G.93, S.94, G.95, A.117, R.260, H.309, W.312, M.321 Ligands: NAD.13 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:Y.70, D:W.312 Hydrogen bonds: D:S.94, D:G.95 Salt bridges: D:R.91, D:R.260, D:H.309 pi-Stacking: D:W.312, D:W.312 pi-Cation interactions: D:R.91

4 x CA: CALCIUM ION(Non-functional Binders)

CA.3: 1 residues within 4Å: Ligands: FMT.4 No protein-ligand interaction detected (PLIP) CA.7: 1 residues within 4Å: Ligands: FMT.8 No protein-ligand interaction detected (PLIP) CA.11: 1 residues within 4Å: Ligands: FMT.12 No protein-ligand interaction detected (PLIP) CA.15: 1 residues within 4Å: Ligands: FMT.16 No protein-ligand interaction detected (PLIP)

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.4: 7 residues within 4Å: Chain A: Y.134, E.169, D.225, G.252, F.254, R.279 Ligands: CA.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.134, A:E.169, A:R.279 FMT.8: 7 residues within 4Å: Chain B: Y.134, E.169, D.225, G.252, F.254, R.279 Ligands: CA.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.134, B:E.169, B:R.279 FMT.12: 7 residues within 4Å: Chain C: Y.134, E.169, D.225, G.252, F.254, R.279 Ligands: CA.11 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.169, C:R.279 Water bridges: C:D.225 FMT.16: 7 residues within 4Å: Chain D: Y.134, E.169, D.225, G.252, F.254, R.279 Ligands: CA.15 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.169, D:R.279 Water bridges: D:D.225

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilbert, B.J. et al., Structure-Guided Design of a High Affinity Inhibitor to Human CtBP. Acs Chem.Biol. (2015)

Release Date

2015-02-11

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

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