SMTL ID : 6u8h.1

BRD2-BD1 in complex with the cyclic peptide 3.2_2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

hetero-1-1-mer

Ligands

6 x IOD: IODIDE ION(Non-functional Binders)

IOD.1: 2 residues within 4Å: Chain A: Q.36, W.39 Ligand excluded by PLIP IOD.2: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.3: 2 residues within 4Å: Chain A: K.30, K.69 Ligand excluded by PLIP IOD.7: 1 residues within 4Å: Chain A: Q.43 Ligand excluded by PLIP IOD.8: 4 residues within 4Å: Chain B: S.3, W.4 Ligands: IOD.9, PE3.10 Ligand excluded by PLIP IOD.9: 1 residues within 4Å: Ligands: IOD.8 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: H.35, Q.36, W.39, R.42 Ligands: PE3.10 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.35, A:W.39, A:R.42, A:R.42 Water bridges: A:Q.36, A:W.39, A:R.42 GOL.5: 4 residues within 4Å: Chain A: Q.43, P.44, D.46, K.49 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.44, A:D.46 Water bridges: A:D.46

1 x NH2: AMINO GROUP(Non-functional Binders)

NH2.6: 4 residues within 4Å: Chain B: N.10, L.11, I.12, H.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.11

1 x PE3: 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL(Non-functional Binders)

PE3.10: 9 residues within 4Å: Chain A: W.39, Q.43 Chain B: X.1, W.2, S.3, W.4, K.7 Ligands: GOL.4, IOD.8 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.7 Water bridges: A:Q.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Patel, K. et al., Cyclic peptides can engage a single binding pocket through highly divergent modes. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-08-19

Peptides

Bromodomain-containing protein 2: A
cyclic peptide 3.2_2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Bromodomain-containing protein 2

cyclic peptide 3.2_2

Related Entries With Identical Sequence