SMTL ID : 7xx7.1

Crystal Structure of Nucleosome-H1x Linker Histone Assembly (sticky-169a DNA fragment)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-4-4-4-4-2-mer

Ligands

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

CL.1: 3 residues within 4Å: Chain A: M.123, P.124, K.125 Ligand excluded by PLIP CL.4: 6 residues within 4Å: Chain C: G.47, A.48, G.49, A.50 Chain D: T.93, S.94 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain E: P.124, K.125 Ligand excluded by PLIP CL.11: 6 residues within 4Å: Chain G: G.47, A.48, G.49, A.50 Chain H: T.93, S.94 Ligand excluded by PLIP CL.32: 3 residues within 4Å: Chain K: M.123, P.124, K.125 Ligand excluded by PLIP CL.34: 6 residues within 4Å: Chain M: G.47, A.48, G.49, A.50 Chain N: T.93, S.94 Ligand excluded by PLIP CL.37: 3 residues within 4Å: Chain O: M.123, P.124, K.125 Ligand excluded by PLIP CL.41: 6 residues within 4Å: Chain Q: G.47, A.48, G.49, A.50 Chain R: T.93, S.94 Ligand excluded by PLIP

51 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.3: 1 residues within 4Å: Chain D: E.116 No protein-ligand interaction detected (PLIP) CA.6: 2 residues within 4Å: Chain C: E.67 Chain D: V.51 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:V.51 CA.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.9: 1 residues within 4Å: Chain G: G.25 No protein-ligand interaction detected (PLIP) CA.10: 2 residues within 4Å: Chain G: E.64, D.93 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:E.64 CA.12: 3 residues within 4Å: Chain I: G.31, C.32 Chain J: G.134 No protein-ligand interaction detected (PLIP) CA.13: 2 residues within 4Å: Chain I: G.134 Chain J: G.31 No protein-ligand interaction detected (PLIP) CA.14: 4 residues within 4Å: Chain I: G.42, G.43 Chain J: A.122, C.123 No protein-ligand interaction detected (PLIP) CA.15: 1 residues within 4Å: Chain I: G.112 No protein-ligand interaction detected (PLIP) CA.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.17: 1 residues within 4Å: Chain I: G.131 No protein-ligand interaction detected (PLIP) CA.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.22: 2 residues within 4Å: Chain I: G.34 Chain J: G.131 No protein-ligand interaction detected (PLIP) CA.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.24: 2 residues within 4Å: Chain J: C.35, T.36 No protein-ligand interaction detected (PLIP) CA.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.26: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.27: 1 residues within 4Å: Chain J: G.34 No protein-ligand interaction detected (PLIP) CA.28: 2 residues within 4Å: Chain J: C.26, C.27 No protein-ligand interaction detected (PLIP) CA.29: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.30: 2 residues within 4Å: Chain J: A.111, G.112 No protein-ligand interaction detected (PLIP) CA.33: 1 residues within 4Å: Chain S: A.69 No protein-ligand interaction detected (PLIP) CA.36: 2 residues within 4Å: Chain M: E.67 Chain N: V.51 2 PLIP interactions: 1 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:V.51, H2O.3 CA.38: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.39: 3 residues within 4Å: Chain Q: E.64, D.93 Chain R: L.109 No protein-ligand interaction detected (PLIP) CA.40: 3 residues within 4Å: Chain Q: E.124 Chain S: G.151, T.152 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:E.124 CA.42: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.43: 3 residues within 4Å: Chain S: G.134, C.135 Chain T: G.31 No protein-ligand interaction detected (PLIP) CA.44: 3 residues within 4Å: Chain S: G.31, C.32 Chain T: G.134 No protein-ligand interaction detected (PLIP) CA.45: 3 residues within 4Å: Chain S: G.59, C.60 Chain T: G.106 No protein-ligand interaction detected (PLIP) CA.46: 2 residues within 4Å: Chain S: G.145, G.146 No protein-ligand interaction detected (PLIP) CA.47: 1 residues within 4Å: Chain S: G.112 No protein-ligand interaction detected (PLIP) CA.48: 2 residues within 4Å: Chain S: G.80, G.81 No protein-ligand interaction detected (PLIP) CA.49: 3 residues within 4Å: Chain S: G.93, C.94 Chain T: G.72 No protein-ligand interaction detected (PLIP) CA.50: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.51: 1 residues within 4Å: Chain S: G.131 No protein-ligand interaction detected (PLIP) CA.52: 1 residues within 4Å: Chain S: G.23 No protein-ligand interaction detected (PLIP) CA.53: 2 residues within 4Å: Chain S: T.66, T.67 No protein-ligand interaction detected (PLIP) CA.54: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.55: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.56: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.57: 3 residues within 4Å: Chain Q: T.123 Chain S: T.152, G.153 No protein-ligand interaction detected (PLIP) CA.60: 1 residues within 4Å: Chain T: G.23 No protein-ligand interaction detected (PLIP) CA.61: 1 residues within 4Å: Chain T: G.112 No protein-ligand interaction detected (PLIP) CA.62: 2 residues within 4Å: Chain T: G.80, G.81 No protein-ligand interaction detected (PLIP) CA.63: 2 residues within 4Å: Chain T: G.42, G.43 No protein-ligand interaction detected (PLIP) CA.64: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.65: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.66: 2 residues within 4Å: Chain S: G.101 Chain T: T.66 No protein-ligand interaction detected (PLIP)

8 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)

K.5: 2 residues within 4Å: Chain C: N.41 Chain G: N.41 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:N.41 K.20: 3 residues within 4Å: Chain I: T.57, A.58 Chain J: A.111 No protein-ligand interaction detected (PLIP) K.21: 1 residues within 4Å: Chain I: A.119 No protein-ligand interaction detected (PLIP) K.31: 3 residues within 4Å: Chain I: A.111 Chain J: T.57, A.58 No protein-ligand interaction detected (PLIP) K.35: 2 residues within 4Å: Chain M: N.41 Chain Q: N.41 2 PLIP interactions: 1 interactions with chain Q, 1 interactions with chain M Metal complexes: Q:N.41, M:N.41 K.58: 3 residues within 4Å: Chain S: T.57, A.58 Chain T: A.111 No protein-ligand interaction detected (PLIP) K.59: 1 residues within 4Å: Chain S: A.119 No protein-ligand interaction detected (PLIP) K.67: 3 residues within 4Å: Chain S: A.111 Chain T: T.57, A.58 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Adhireksan, Z. et al., Diversity in Linker Histone-Nucleosome Interactions Between and Within Variants. To Be Published

Release Date

2023-05-31

Peptides

Histone H3.1: AEKO
Histone H4: BFLP
Histone H2A type 1-B/E: CGMQ
Histone H2B type 1-J: DHNR
Histone H1.10: UV

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

K
K

O
O

B
B

F
F

L
L

P
P

C
C

G
G

M
M

Q
Q

D
D

H
H

N
N

R
R

U
U

V
V

Histone H3.1

Histone H4

Histone H2A type 1-B/E

Histone H2B type 1-J

Histone H1.10

Related Entries With Identical Sequence