SMTL ID : 7rjp.1

Crystal structure of human Bromodomain containing protein 4 (BRD4) in complex with SHMT

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

monomer

Ligands

1 x ARG- ALY- GLY- VAL- ALY- SER: Serine hydroxymethyltransferase, cytosolic(Non-covalent)

ARG-ALY-GLY-VAL-ALY-SER.1: 18 residues within 4Å: Chain A: W.40, P.41, F.42, V.46, L.51, L.53, D.55, Y.56, I.59, C.95, I.97, Y.98, N.99, D.103, D.104, I.105, M.108 Ligands: CL.15 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:W.40, A:W.40, A:W.40, A:V.46, A:L.51, A:L.53, A:Y.98, A:D.104 Hydrogen bonds: A:Y.98, A:N.99, A:N.99, A:D.103, A:D.104, A:D.104, A:D.104 Water bridges: A:Y.56, A:D.103, A:D.103, A:D.104 Salt bridges: A:D.55

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

EDO.2: 7 residues within 4Å: Chain A: I.59, I.60, K.61, T.62, T.90, N.94, I.97 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.59, A:K.61, A:T.62, A:T.62, A:N.94

8 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: L.22, Q.23, L.26, L.73 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.73 NA.4: 1 residues within 4Å: Chain A: K.61 No protein-ligand interaction detected (PLIP) NA.5: 4 residues within 4Å: Chain A: G.102, D.103, V.106, L.107 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.102, A:G.102, A:L.107 NA.6: 6 residues within 4Å: Chain A: P.15, K.16, R.17, N.76, Y.78, W.79 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.17, A:R.17 NA.7: 7 residues within 4Å: Chain A: P.45, V.46, Y.56, Y.57, P.63, M.64 Ligands: NA.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.46, A:Y.57 NA.8: 7 residues within 4Å: Chain A: V.46, Y.56, I.60, P.63, M.64, N.94 Ligands: NA.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.56, A:M.64, A:N.94 NA.9: 2 residues within 4Å: Chain A: R.27, K.31 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.27 NA.10: 2 residues within 4Å: Chain A: H.36, Q.37 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.36, A:Q.37

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 2 residues within 4Å: Chain A: R.17, Q.18 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: Y.57, K.58, K.61 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain A: H.36, Q.37, A.39, W.40 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain A: D.103 Ligands: ARG-ALY-GLY-VAL-ALY-SER.1, ARG-ALY-GLY-VAL-ALY-SER.1, ARG-ALY-GLY-VAL-ALY-SER.1 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 1 residues within 4Å: Chain A: P.124 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wagner, S. et al., Uncovering the Bromodomain Interactome using Site-Specific Azide-Acetyllysine Photochemistry, Proteomic Profiling and Structural Characterization. To Be Published

Release Date

2022-08-03

Peptides

Bromodomain-containing protein 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bromodomain-containing protein 4

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