SMTL ID : 6cdr.1 (1 other biounit)

Human CtBP1 (28-378)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.1: 35 residues within 4Å: Chain A: S.94, G.95, S.118, T.122, I.174, G.175, L.176, G.177, R.178, V.179, G.180, Y.197, D.198, P.199, Y.200, L.201, H.230, C.231, G.232, L.233, N.234, N.237, L.240, T.258, A.259, R.260, D.284, V.285, H.309, A.310, A.311, W.312 Ligands: CL.2, EDO.5, FMT.8 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:T.122, A:W.312 Hydrogen bonds: A:G.95, A:G.177, A:R.178, A:V.179, A:G.232, A:N.234, A:N.237, A:D.284, A:D.284, A:A.311, A:W.312 Water bridges: A:R.178, A:R.178, A:G.180, A:Y.200, A:Y.200 Salt bridges: A:R.178 pi-Stacking: A:Y.200 NAI.9: 35 residues within 4Å: Chain B: S.94, G.95, S.118, T.122, I.174, G.175, L.176, G.177, R.178, V.179, G.180, Y.197, D.198, P.199, Y.200, L.201, H.230, C.231, G.232, L.233, N.234, N.237, L.240, T.258, A.259, R.260, D.284, V.285, H.309, A.310, A.311, W.312 Ligands: CL.10, EDO.13, FMT.16 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:T.122, B:W.312 Hydrogen bonds: B:G.95, B:G.177, B:R.178, B:V.179, B:G.232, B:N.234, B:N.237, B:D.284, B:D.284, B:A.311, B:W.312 Water bridges: B:R.178, B:R.178, B:G.180, B:Y.200, B:Y.200 Salt bridges: B:R.178 pi-Stacking: B:Y.200 NAI.17: 35 residues within 4Å: Chain C: S.94, G.95, S.118, T.122, I.174, G.175, L.176, G.177, R.178, V.179, G.180, Y.197, D.198, P.199, Y.200, L.201, H.230, C.231, G.232, L.233, N.234, N.237, L.240, T.258, A.259, R.260, D.284, V.285, H.309, A.310, A.311, W.312 Ligands: CL.18, EDO.21, FMT.24 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:T.122, C:W.312 Hydrogen bonds: C:G.95, C:G.177, C:R.178, C:V.179, C:G.232, C:N.234, C:N.237, C:D.284, C:A.311, C:W.312 Water bridges: C:R.178, C:R.178, C:G.180, C:Y.200, C:Y.200 Salt bridges: C:R.178 pi-Stacking: C:Y.200 NAI.25: 35 residues within 4Å: Chain D: S.94, G.95, S.118, T.122, I.174, G.175, L.176, G.177, R.178, V.179, G.180, Y.197, D.198, P.199, Y.200, L.201, H.230, C.231, G.232, L.233, N.234, N.237, L.240, T.258, A.259, R.260, D.284, V.285, H.309, A.310, A.311, W.312 Ligands: CL.26, EDO.29, FMT.32 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:T.122, D:W.312 Hydrogen bonds: D:G.95, D:G.177, D:R.178, D:V.179, D:G.232, D:N.234, D:N.237, D:D.284, D:A.311, D:W.312 Water bridges: D:R.178, D:R.178, D:G.180, D:Y.200, D:Y.200 Salt bridges: D:R.178 pi-Stacking: D:Y.200

8 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 4 residues within 4Å: Chain A: R.91, R.260, H.309 Ligands: NAI.1 Ligand excluded by PLIP CL.3: 1 residues within 4Å: Chain A: Q.212 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: R.91, R.260, H.309 Ligands: NAI.9 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain B: Q.212 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain C: R.91, R.260, H.309 Ligands: NAI.17 Ligand excluded by PLIP CL.19: 1 residues within 4Å: Chain C: Q.212 Ligand excluded by PLIP CL.26: 4 residues within 4Å: Chain D: R.91, R.260, H.309 Ligands: NAI.25 Ligand excluded by PLIP CL.27: 1 residues within 4Å: Chain D: Q.212 Ligand excluded by PLIP

16 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 8 residues within 4Å: Chain A: Y.70, H.71, R.91, I.92, G.93, W.312, M.321 Chain D: V.153 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: S.94, G.95, F.96, N.113, P.115, R.178, G.232 Ligands: NAI.1 Ligand excluded by PLIP EDO.6: 9 residues within 4Å: Chain A: Y.134, G.162, A.164, E.169, D.225, G.252, A.253, F.254, R.279 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: D.97, N.98, L.233, R.260, G.262, E.287 Ligand excluded by PLIP EDO.12: 8 residues within 4Å: Chain B: Y.70, H.71, R.91, I.92, G.93, W.312, M.321 Chain C: V.153 Ligand excluded by PLIP EDO.13: 8 residues within 4Å: Chain B: S.94, G.95, F.96, N.113, P.115, R.178, G.232 Ligands: NAI.9 Ligand excluded by PLIP EDO.14: 9 residues within 4Å: Chain B: Y.134, G.162, A.164, E.169, D.225, G.252, A.253, F.254, R.279 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain B: D.97, N.98, L.233, R.260, G.262, E.287 Ligand excluded by PLIP EDO.20: 8 residues within 4Å: Chain B: V.153 Chain C: Y.70, H.71, R.91, I.92, G.93, W.312, M.321 Ligand excluded by PLIP EDO.21: 8 residues within 4Å: Chain C: S.94, G.95, F.96, N.113, P.115, R.178, G.232 Ligands: NAI.17 Ligand excluded by PLIP EDO.22: 9 residues within 4Å: Chain C: Y.134, G.162, A.164, E.169, D.225, G.252, A.253, F.254, R.279 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain C: D.97, N.98, L.233, R.260, G.262, E.287 Ligand excluded by PLIP EDO.28: 8 residues within 4Å: Chain A: V.153 Chain D: Y.70, H.71, R.91, I.92, G.93, W.312, M.321 Ligand excluded by PLIP EDO.29: 8 residues within 4Å: Chain D: S.94, G.95, F.96, N.113, P.115, R.178, G.232 Ligands: NAI.25 Ligand excluded by PLIP EDO.30: 9 residues within 4Å: Chain D: Y.134, G.162, A.164, E.169, D.225, G.252, A.253, F.254, R.279 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain D: D.97, N.98, L.233, R.260, G.262, E.287 Ligand excluded by PLIP

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

FMT.8: 3 residues within 4Å: Chain A: Y.200, N.234 Ligands: NAI.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.234 FMT.16: 3 residues within 4Å: Chain B: Y.200, N.234 Ligands: NAI.9 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.234 FMT.24: 3 residues within 4Å: Chain C: Y.200, N.234 Ligands: NAI.17 1 PLIP interactions: 1 interactions with chain C Water bridges: C:N.234 FMT.32: 3 residues within 4Å: Chain D: Y.200, N.234 Ligands: NAI.25 1 PLIP interactions: 1 interactions with chain D Water bridges: D:N.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bellesis, A.G. et al., Assembly of human C-terminal binding protein (CtBP) into tetramers. J. Biol. Chem. (2018)

Release Date

2018-05-09

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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