SMTL ID : 7slw.1 (1 other biounit)

Complex structure of CDYL2 with an antagonist

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

3 x 5R0- PHE- ALA- LEU- 9RI- SER: Chromodomain Y-like protein 2(Non-covalent)

5R0-PHE-ALA-LEU-9RI-SER.1: 22 residues within 4Å: Chain A: G.4, D.5, L.6, Y.7, E.8, V.9, W.29, Y.32, E.36, T.38, E.40, H.44, L.46, H.47, C.48, E.50, F.51 Chain B: S.3, H.43, H.44 Ligands: 5R0-PHE-ALA-LEU-9RI-SER.2, 5R0-PHE-ALA-LEU-9RI-SER.3 22 PLIP interactions: 20 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.6, A:Y.7, A:V.9, A:W.29, A:W.29, A:Y.32, A:H.44, A:E.50, A:F.51, B:S.3 Hydrogen bonds: A:D.5, A:Y.7, A:Y.7, A:V.9, A:E.40, A:H.44, A:H.44, A:L.46, A:L.46 pi-Stacking: A:F.51, B:H.43 pi-Cation interactions: A:Y.7 5R0-PHE-ALA-LEU-9RI-SER.2: 22 residues within 4Å: Chain A: L.6 Chain B: G.4, D.5, L.6, Y.7, E.8, V.9, W.29, Y.32, E.40, H.44, L.45, L.46, H.47, C.48, E.50, F.51 Chain C: H.43, H.44, L.46 Ligands: 5R0-PHE-ALA-LEU-9RI-SER.1, 5R0-PHE-ALA-LEU-9RI-SER.3 24 PLIP interactions: 22 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: B:L.6, B:L.6, B:Y.7, B:V.9, B:W.29, B:W.29, B:Y.32, B:L.45, B:L.46, B:L.46, B:E.50, B:F.51, A:L.6 Hydrogen bonds: B:D.5, B:Y.7, B:Y.7, B:V.9, B:E.40, B:H.44, B:H.44, B:L.46, B:L.46 pi-Cation interactions: B:Y.7 pi-Stacking: C:H.43 5R0-PHE-ALA-LEU-9RI-SER.3: 21 residues within 4Å: Chain A: S.3, H.43, H.44 Chain C: G.4, D.5, L.6, Y.7, E.8, V.9, W.29, Y.32, E.36, E.40, H.44, L.46, H.47, C.48, E.50, F.51 Ligands: 5R0-PHE-ALA-LEU-9RI-SER.1, 5R0-PHE-ALA-LEU-9RI-SER.2 21 PLIP interactions: 19 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:Y.7, C:E.8, C:V.9, C:W.29, C:W.29, C:Y.32, C:H.44, C:F.51, A:H.43 Hydrogen bonds: C:D.5, C:Y.7, C:Y.7, C:V.9, C:E.40, C:H.44, C:L.46, C:L.46 Salt bridges: C:E.36 pi-Stacking: C:F.51, A:H.43 pi-Cation interactions: C:Y.7

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: L.46, H.47 Chain B: L.46, H.47, E.49 Chain C: H.47 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.47, B:H.47, A:H.47

1 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.5: 3 residues within 4Å: Chain C: L.45, H.47, C.48 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Beldar, S. et al., Complex structure of CDYL2 with an antagonist. To Be Published

Release Date

2021-11-17

Peptides

Chromodomain Y-like protein 2: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Chromodomain Y-like protein 2

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