SMTL ID : 5s8q.2 (1 other biounit)

XChem group deposition -- Crystal Structure of the second bromodomain of pleckstrin homology domain interacting protein (PHIP) in complex with FMO3D000185a (space group P212121)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x XLY: (3R)-3-methyl-1,2,3,4-tetrahydro-5H-1,4-benzodiazepin-5-one(Non-covalent)

XLY.1: 11 residues within 4Å: Chain A: P.28, F.29, Q.31, V.33, Y.38, Y.41, M.49, D.50, N.79, S.80, I.91 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.29, A:V.33, A:D.50, A:I.91 Water bridges: A:P.32, A:D.34

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

CA.2: 3 residues within 4Å: Ligands: EDO.7, EDO.8, EDO.9 No protein-ligand interaction detected (PLIP) CA.3: 3 residues within 4Å: Ligands: EDO.4, EDO.5, EDO.6 No protein-ligand interaction detected (PLIP)

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

EDO.4: 8 residues within 4Å: Chain A: N.62, Y.63, E.68, D.72 Ligands: CA.3, EDO.5, EDO.6, EDO.7 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.72, A:D.72 EDO.5: 6 residues within 4Å: Chain A: T.47, M.49, D.72 Ligands: CA.3, EDO.4, EDO.6 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.72, A:D.72, A:D.72 EDO.6: 6 residues within 4Å: Chain A: M.49, T.57, D.72 Ligands: CA.3, EDO.4, EDO.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.72 EDO.7: 4 residues within 4Å: Ligands: CA.2, EDO.4, EDO.8, EDO.9 No protein-ligand interaction detected (PLIP) EDO.8: 4 residues within 4Å: Chain A: N.62 Ligands: CA.2, EDO.7, EDO.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.62 EDO.9: 4 residues within 4Å: Chain A: E.64 Ligands: CA.2, EDO.7, EDO.8 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krojer, T. et al., XChem group deposition. To Be Published

Release Date

2021-01-13

Peptides

PH-interacting protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

PH-interacting protein

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