SMTL ID : 8rwz.1

Open non-crosslinked structure Brd4BD2-MZ1-(NEDD8)-CRL2VHL

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-mer

Ligands

1 x 759: (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide(Covalent)

759.1: 24 residues within 4Å: Chain A: W.42, V.48, D.49, A.52, L.53, G.54, L.55, Y.58, C.97, Y.100, N.101, H.105, V.107 Chain B: W.35, F.38, Q.43, Y.45, P.46, T.47, R.54, I.56, H.57, H.62, W.64 14 PLIP interactions: 4 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:L.53, A:V.107, B:W.35, B:W.35, B:Q.43, B:Y.45, B:Y.45, B:P.46, B:W.64 Hydrogen bonds: A:H.105, B:Y.45, B:H.57, B:H.57 pi-Cation interactions: A:H.105

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain F: C.51, C.54, S.63, C.66, H.80 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.51, F:C.54, F:H.80 ZN.3: 5 residues within 4Å: Chain F: C.40, C.43, C.51, H.78, C.81 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.43, F:H.78, F:C.81 ZN.4: 4 residues within 4Å: Chain F: C.73, N.74, H.75, D.95 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.73, F:H.75, F:D.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ciulli, A. et al., Open non-crosslinked structure Brd4BD2-MZ1-(NEDD8)-CRL2VHL. To Be Published

Release Date

2024-03-06

Peptides

Bromodomain-containing protein 4: A
von Hippel-Lindau disease tumor suppressor: B
Elongin-B: C
Elongin-C: D
Cullin-2: E
Rbx1: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
R

Bromodomain-containing protein 4

von Hippel-Lindau disease tumor suppressor

Elongin-B

Elongin-C

Cullin-2

Rbx1

Related Entries With Identical Sequence