SMTL ID : 7xvm.1

Crystal Structure of Nucleosome-H5 Linker Histone Assembly (sticky-169a DNA fragment)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.84 Å

Oligo State

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

Ligands

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

CA.1: 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.4: 2 residues within 4Å: Chain I: G.134 Chain J: G.31 No protein-ligand interaction detected (PLIP) CA.5: 2 residues within 4Å: Chain I: G.31 Chain J: G.134 No protein-ligand interaction detected (PLIP) CA.6: 2 residues within 4Å: Chain I: G.80, G.81 No protein-ligand interaction detected (PLIP) CA.7: 1 residues within 4Å: Chain I: G.112 No protein-ligand interaction detected (PLIP) CA.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.10: 1 residues within 4Å: Chain I: C.26 No protein-ligand interaction detected (PLIP) CA.11: 1 residues within 4Å: Chain I: G.80 No protein-ligand interaction detected (PLIP) CA.13: 1 residues within 4Å: Chain J: G.112 No protein-ligand interaction detected (PLIP) CA.14: 1 residues within 4Å: Chain J: G.49 No protein-ligand interaction detected (PLIP) CA.15: 1 residues within 4Å: Chain J: G.43 No protein-ligand interaction detected (PLIP) CA.17: 3 residues within 4Å: Chain S: G.53, C.54 Chain T: G.112 No protein-ligand interaction detected (PLIP) CA.18: 3 residues within 4Å: Chain S: G.31, C.32 Chain T: G.134 No protein-ligand interaction detected (PLIP) CA.19: 2 residues within 4Å: Chain S: G.134 Chain T: G.31 No protein-ligand interaction detected (PLIP) CA.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.22: 3 residues within 4Å: Chain S: A.50 Chain T: G.115, T.116 No protein-ligand interaction detected (PLIP)

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

CL.2: 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.3: 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.16: 6 residues within 4Å: Chain M: G.47, A.48, G.49, A.50 Chain N: T.93, S.94 Ligand excluded by PLIP

2 x K: POTASSIUM ION(Non-functional Binders)

K.12: 3 residues within 4Å: Chain I: T.57, A.58 Chain J: A.111 No protein-ligand interaction detected (PLIP) K.23: 2 residues within 4Å: 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., Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169a DNA fragment). To Be Published

Release Date

2023-05-24

Peptides

Histone H3.1: AEKO
Histone H4: BFLP
Histone H2A type 1-B/E: CGMQ
Histone H2B type 1-J: DHNR
Histone H5: 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 H5

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