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Crystal structure of the human BRD2 BD1 bromodomain in complex with a BRD2-interactive compound, BIC1

X-ray diffraction
2.3Å resolution
PDB entry 3aqa coloured by chain, front view.
PDB entry 3aqa coloured by chain, side view.
PDB entry 3aqa coloured by chain, top view.
Source organism: Homo sapiens
Assemblies composition:
monomeric (preferred)
homo dimer
Entry contents: 1 distinct polypeptide molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Bromodomain-containing protein 2
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Multimeric state: monomeric
Accessible surface area: 6828.64 Å2
Buried surface area: 200.7 Å2
Dissociation area: 100.35 Å2
Dissociation energy (ΔGdiss): -3.75 kcal/mol
Dissociation entropy (TΔSdiss): 2.79 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-150461
Monomeric assembly 1 of PDB entry 3aqa coloured by chemically distinct molecules, front view.
Monomeric assembly 1 of PDB entry 3aqa coloured by chemically distinct molecules, side view.
Monomeric assembly 1 of PDB entry 3aqa coloured by chemically distinct molecules, top view.
    Assembly 1
Confidence : 12%
No. subunits : 1
Symmetry : None
More details
3DComplex & QSbio predictionx
No. subunits : 2
Symmetry : C2
Evidence : Sequence is/are identical to 3aqa_5 (which is supposedly correct) suggesting that interface(s) is/are missing
Assembly 2
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Assembly Name: Bromodomain-containing protein 2
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Multimeric state: monomeric
Accessible surface area: 7394.39 Å2
Buried surface area: 0.0 Å2
Dissociation area: 0 Å2
Dissociation energy (ΔGdiss): 0 kcal/mol
Dissociation entropy (TΔSdiss): 0 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-150461
Monomeric assembly 2 of PDB entry 3aqa coloured by chemically distinct molecules, front view.
Monomeric assembly 2 of PDB entry 3aqa coloured by chemically distinct molecules, side view.
Monomeric assembly 2 of PDB entry 3aqa coloured by chemically distinct molecules, top view.
    Assembly 2
Confidence : 12%
No. subunits : 1
Symmetry : None
More details
3DComplex & QSbio predictionx
No. subunits : 2
Symmetry : C2
Evidence : Sequence is/are identical to 3aqa_5 (which is supposedly correct) suggesting that interface(s) is/are missing
Assembly 3
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Assembly Name: Bromodomain-containing protein 2
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Multimeric state: monomeric
Accessible surface area: 6717.74 Å2
Buried surface area: 0.0 Å2
Dissociation area: 0 Å2
Dissociation energy (ΔGdiss): 0 kcal/mol
Dissociation entropy (TΔSdiss): 0 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-150461
Monomeric assembly 3 of PDB entry 3aqa coloured by chemically distinct molecules, front view.
Monomeric assembly 3 of PDB entry 3aqa coloured by chemically distinct molecules, side view.
Monomeric assembly 3 of PDB entry 3aqa coloured by chemically distinct molecules, top view.
    Assembly 3
Confidence : 12%
No. subunits : 1
Symmetry : None
More details
3DComplex & QSbio predictionx
No. subunits : 2
Symmetry : C2
Evidence : Sequence is/are identical to 3aqa_5 (which is supposedly correct) suggesting that interface(s) is/are missing
Assembly 4
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Assembly Name: Bromodomain-containing protein 2
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Multimeric state: homo dimer
Accessible surface area: 12150.28 Å2
Buried surface area: 2273.45 Å2
Dissociation area: 1,036.38 Å2
Dissociation energy (ΔGdiss): 4.77 kcal/mol
Dissociation entropy (TΔSdiss): 11.71 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-150468
Homo dimeric assembly 4 of PDB entry 3aqa coloured by chemically distinct molecules, front view.
Homo dimeric assembly 4 of PDB entry 3aqa coloured by chemically distinct molecules, side view.
Homo dimeric assembly 4 of PDB entry 3aqa coloured by chemically distinct molecules, top view.
    Assembly 4
Confidence : 98%
No. subunits : 2
Symmetry : C2
More details
3DComplex & QSbio predictionx
No. subunits : 2
Symmetry : C2
Evidence : Interface geometry is similar to that of 4kcx_1 (67% id)
Assembly 5
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Assembly Name: Bromodomain-containing protein 2
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Multimeric state: homo dimer
Accessible surface area: 11317.13 Å2
Buried surface area: 2124.8 Å2
Dissociation area: 1,062.4 Å2
Dissociation energy (ΔGdiss): 2.46 kcal/mol
Dissociation entropy (TΔSdiss): 11.54 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-150468
Homo dimeric assembly 5 of PDB entry 3aqa coloured by chemically distinct molecules, front view.
Homo dimeric assembly 5 of PDB entry 3aqa coloured by chemically distinct molecules, side view.
Homo dimeric assembly 5 of PDB entry 3aqa coloured by chemically distinct molecules, top view.
    Assembly 5
Confidence : 98%
No. subunits : 2
Symmetry : C2
More details
3DComplex & QSbio predictionx
No. subunits : 2
Symmetry : C2
Evidence : Interface geometry is similar to that of 4kcx_1 (67% id)

Macromolecules

Bromodomain-containing protein 2
Chains: A, B, C
Length: 128 amino acids
Theoretical weight: 15.26 KDa
Source organism: Homo sapiens
Expression system: bacterial cell free system
UniProt:
  • Canonical: P25440 (Residues: 73-194; Coverage: 15%)
Gene names: BRD2, KIAA9001, RING3
Pfam: Bromodomain
InterPro:
CATH: Bromodomain-like
Bromodomain-containing protein 2 in PDB entry 3aqa, assembly 1, front view.
Bromodomain-containing protein 2 in PDB entry 3aqa, assembly 1, side view.
Bromodomain-containing protein 2 in PDB entry 3aqa, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P25440  
1128102030405060708090100110120
 
50100
UniProt
P25440
Chains
Domains
Secondary structure
Flexibility predictions
Early folding residue predictions
Ligand binding sites
Sequence conservation
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