PDB 4lsj biological assemblies and structure analysis ‹ Protein Data Bank in Europe (PDBe)

Assemblies

Assembly 1

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Assembly Name: Glucocorticoid receptor and peptide
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Multimeric state: hetero tetramer

Accessible surface area: 23989.65 Å²

Buried surface area: 7590.74 Å²

Dissociation area: 1,121.96 Å²

Dissociation energy (ΔG^diss): 10.63 kcal/mol

Dissociation entropy (TΔS^diss): 14.19 kcal/mol

Symmetry number: 2

PDBe Complex ID: PDB-CPX-137450

$Hetero tetrameric assembly 1 of PDB entry 4lsj coloured by chemically distinct molecules, front view. This structure contains: <ul class='image_legend_ul'><li class='image_legend_li'>2 copies of Glucocorticoid receptor;</li> <li class='image_legend_li'>2 copies of D30 peptide;</li> <li class='image_legend_li'>4 copies of N-{3-[(1Z)-1-(10-methoxydibenzo[b,e]oxepin-11(6H)-ylidene)propyl]phenyl}methanesulfonamide;</li> <li class='image_legend_li'>2 copies of water.</li></ul>}$

$Hetero tetrameric assembly 1 of PDB entry 4lsj coloured by chemically distinct molecules, side view. This structure contains: <ul class='image_legend_ul'><li class='image_legend_li'>2 copies of Glucocorticoid receptor;</li> <li class='image_legend_li'>2 copies of D30 peptide;</li> <li class='image_legend_li'>4 copies of N-{3-[(1Z)-1-(10-methoxydibenzo[b,e]oxepin-11(6H)-ylidene)propyl]phenyl}methanesulfonamide;</li> <li class='image_legend_li'>2 copies of water.</li></ul>}$

$Hetero tetrameric assembly 1 of PDB entry 4lsj coloured by chemically distinct molecules, top view. This structure contains: <ul class='image_legend_ul'><li class='image_legend_li'>2 copies of Glucocorticoid receptor;</li> <li class='image_legend_li'>2 copies of D30 peptide;</li> <li class='image_legend_li'>4 copies of N-{3-[(1Z)-1-(10-methoxydibenzo[b,e]oxepin-11(6H)-ylidene)propyl]phenyl}methanesulfonamide;</li> <li class='image_legend_li'>2 copies of water.</li></ul>}$

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Assembly 2 (preferred)

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Assembly Name: Glucocorticoid receptor and peptide
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Multimeric state: hetero dimer

Accessible surface area: 14683.22 Å²

Buried surface area: 1103.05 Å²

Dissociation area: 551.52 Å²

Dissociation energy (ΔG^diss): 5.63 kcal/mol

Dissociation entropy (TΔS^diss): 7.06 kcal/mol

Symmetry number: 1

PDBe Complex ID: PDB-CPX-137444

$Hetero dimeric assembly 2 of PDB entry 4lsj coloured by chemically distinct molecules, front view. This structure contains: <ul class='image_legend_ul'><li class='image_legend_li'>1 copy of Glucocorticoid receptor;</li> <li class='image_legend_li'>1 copy of D30 peptide;</li> <li class='image_legend_li'>2 copies of N-{3-[(1Z)-1-(10-methoxydibenzo[b,e]oxepin-11(6H)-ylidene)propyl]phenyl}methanesulfonamide;</li> <li class='image_legend_li'>1 copy of water.</li></ul>}$

$Hetero dimeric assembly 2 of PDB entry 4lsj coloured by chemically distinct molecules, side view. This structure contains: <ul class='image_legend_ul'><li class='image_legend_li'>1 copy of Glucocorticoid receptor;</li> <li class='image_legend_li'>1 copy of D30 peptide;</li> <li class='image_legend_li'>2 copies of N-{3-[(1Z)-1-(10-methoxydibenzo[b,e]oxepin-11(6H)-ylidene)propyl]phenyl}methanesulfonamide;</li> <li class='image_legend_li'>1 copy of water.</li></ul>}$

$Hetero dimeric assembly 2 of PDB entry 4lsj coloured by chemically distinct molecules, top view. This structure contains: <ul class='image_legend_ul'><li class='image_legend_li'>1 copy of Glucocorticoid receptor;</li> <li class='image_legend_li'>1 copy of D30 peptide;</li> <li class='image_legend_li'>2 copies of N-{3-[(1Z)-1-(10-methoxydibenzo[b,e]oxepin-11(6H)-ylidene)propyl]phenyl}methanesulfonamide;</li> <li class='image_legend_li'>1 copy of water.</li></ul>}$

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Macromolecules

Glucocorticoid receptor

Chain: A
Length: 258 amino acids
Theoretical weight: 29.94 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:

Canonical: P04150 (Residues: 522-777; Coverage: 33%)

Gene names: GRL, NR3C1
Pfam: Ligand-binding domain of nuclear hormone receptor
InterPro:

Nuclear hormone receptor-like domain superfamily
Nuclear hormone receptor, ligand-binding domain
Nuclear hormone receptor

CATH: Retinoid X Receptor

Glucocorticoid receptor in PDB entry 4lsj, assembly 2, front view.

Glucocorticoid receptor in PDB entry 4lsj, assembly 2, side view.

Glucocorticoid receptor in PDB entry 4lsj, assembly 2, top view.

FASTA Sequence


    >pdb|4lsj|A

SLPATLPQLTPTLVSLLEVIEPEVLYAGYDSSVPDSTWRIMTTLNMLGGRQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMYLMAFALGWRSYRQSSANLLCFAPDLIINEQRMTLPGMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSSVPKDGLKSQELFDEIRMTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEVVENLLNYCFQTFLDKTMSIEFPEMLAEIITNQIPKYSNGNIKKLLFHQK

PDBe-KB: UniProt Coverage View: P04150

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UniProt

P04150

Mapping to UniProt GCR_HUMAN

Chains

RSRZ Outlier Chain A

Chain A

Domains

Residues mapped to CATH domains

Residues mapped to InterPro annotations

Secondary structure

Residues forming Helix

Residues forming Strand

Flexibility predictions

Early folding residue predictions

Ligand binding sites

Residues binding N-{3-[(1Z)-1-(10-methoxydibenzo[b,e]oxepin-11(6H)-ylidene)propyl]phenyl}methanesulfonamide <img src="https://www.ebi.ac.uk/pdbe/static/files/pdbechem_v2/LSJ_200.svg" />

Sequence conservation

Amino acid probabilities The amino acid probabilities are calculated using HMM profiles based on multiple sequence alignments. Click to see more details...

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Amino acid properties

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Molecule details ›

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FASTA (Protein chains A)
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BLAST P04150 (UniProt)

D30 peptide

Chain: B
Length: 13 amino acids
Theoretical weight: 1.57 KDa
Source organism: Homo sapiens
Expression system: Not provided

D30 peptide in PDB entry 4lsj, assembly 2, side view.

D30 peptide in PDB entry 4lsj, assembly 2, top view.

FASTA Sequence


    >pdb|4lsj|B

HSSRLWELLMEAT

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Chains

RSRZ Outlier Chain B (auth B)

RSRZ Outlier Chain B

Chain B (auth B)

Chain B

Secondary structure

Residues forming Helix

Flexibility predictions

Interaction interfaces

Residues interacting with Glucocorticoid receptor (P04150)

Sequence conservation

Amino acid probabilities The amino acid probabilities are calculated using HMM profiles based on multiple sequence alignments. Click to see more details...

Data displayed by

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Probability

Download MSA Click to download the multiple sequence alignment (MSA) file

Amino acid properties

Aromatic

Polar

Hydrophobic

Negative charge

Proline

Positive charge

Cysteine

Glycine

Variants

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Likely disease

Predicted deleteriousPredicted benign

Likely benign

Uncertain

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UniProt reviewed

ClinVar reviewed

Large scale studies

FoldX analysis

Missense3D

Observed in PDB

SKEMPI

FireProtDB

Frustratometer

neXtProt

Molecule details ›

Download

FASTA (Protein chains B)
Archive mmCIF file
Updated mmCIF file
PDB file
PDB header
PDB file (gz)
PDBML
PDBML (ATOM lines)
PDBML (no atoms)
Structure Factors
SIFTS XML file with residue-level mappings

Search similar proteins

Similar 3D structures (PDBeFold)
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Protein Data Bank in Europe

Crystal Structure of the Glucocorticoid Receptor Ligand Binding Domain Bound to a Dibenzoxapine Sulfonamide

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Assemblies

Assembly 1

Assembly 2 (preferred)

Macromolecules

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PDBe › 4lsj › Structure analysis

Crystal Structure of the Glucocorticoid Receptor Ligand Binding Domain Bound to a Dibenzoxapine Sulfonamide

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Assemblies

Assembly 1

Assembly 2 (preferred)

Macromolecules

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4lsj › Structure analysis