SMTL ID : 4zux.1 (1 other biounit)

SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.82 Å

Oligo State

hetero-oligomer

Ligands

16 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain K: C.47, C.50, C.69, H.74 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.47, K:C.50, K:C.69, K:H.74 ZN.2: 4 residues within 4Å: Chain K: C.61, C.64, H.78, H.84 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:C.61, K:C.64, K:H.78 ZN.3: 4 residues within 4Å: Chain K: C.5, H.7, C.97, C.100 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.5, K:H.7, K:C.97, K:C.100 ZN.4: 4 residues within 4Å: Chain K: H.171, C.175, C.183, C.186 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:H.171, K:C.175, K:C.183, K:C.186 ZN.5: 4 residues within 4Å: Chain K: H.251, C.272, C.274, H.277 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:H.251, K:C.272, K:C.274, K:H.277 ZN.6: 4 residues within 4Å: Chain K: C.290, C.293, C.337, C.340 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.290, K:C.293, K:C.337, K:C.340 ZN.7: 5 residues within 4Å: Chain M: C.73, N.75, C.76, H.88, C.92 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:C.73, M:C.76, M:C.92 ZN.8: 4 residues within 4Å: Chain O: C.78, C.81, H.93, C.98 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.78, O:C.81, O:H.93, O:C.98 ZN.9: 4 residues within 4Å: Chain P: C.290, G.292, C.293, C.340 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:C.290, P:C.293, P:C.340 ZN.10: 4 residues within 4Å: Chain P: C.272, E.273, C.274, H.277 2 PLIP interactions: 2 interactions with chain P Metal complexes: P:C.272, P:C.274 ZN.11: 5 residues within 4Å: Chain P: H.171, C.175, R.178, C.183, C.186 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:H.171, P:C.175, P:C.183, P:C.186 ZN.12: 5 residues within 4Å: Chain P: C.5, P.6, H.7, C.97, C.100 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.5, P:H.7, P:C.97, P:C.100 ZN.13: 5 residues within 4Å: Chain P: C.61, Q.63, C.64, H.78, H.84 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.61, P:C.64, P:H.78, P:H.84 ZN.14: 5 residues within 4Å: Chain P: C.47, C.50, C.69, H.72, H.74 5 PLIP interactions: 5 interactions with chain P Metal complexes: P:C.47, P:C.50, P:C.69, P:H.72, P:H.74 ZN.15: 5 residues within 4Å: Chain R: C.73, N.75, C.76, H.88, C.92 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.73, R:C.76, R:H.88, R:C.92 ZN.16: 4 residues within 4Å: Chain T: C.78, C.81, H.93, C.98 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:C.78, T:C.81, T:H.93, T:C.98

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Morgan, M.T. et al., Structural basis for histone H2B deubiquitination by the SAGA DUB module. Science (2016)

Release Date

2016-02-24

Peptides

Histone H3.2: AE
Histone H4: BF
Histone H2A type 1: CG
Histone H2B 1.1: DH
Ubiquitin carboxyl-terminal hydrolase 8: KP
Transcription and mRNA export factor SUS1: LQ
SAGA-associated factor 11: MR
Polyubiquitin-B: NS
SAGA-associated factor 73: OT

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
C

G
G

D
D

H
H

K
U

P
Z

L
V

Q
a

M
W

R
b

N
X

S
c

O
Y

T
d

Histone H3.2

Histone H4

Histone H2A type 1

Histone H2B 1.1

Ubiquitin carboxyl-terminal hydrolase 8

Transcription and mRNA export factor SUS1

SAGA-associated factor 11

Polyubiquitin-B

SAGA-associated factor 73

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