SMTL ID : 9c62.1

P400 subcomplex of the native human TIP60 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-1-1-1-2-1-1-mer

Ligands

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Covalent)(Non-covalent)

ADP.1: 18 residues within 4Å: Chain A: H.25, H.27, M.46, Q.78, P.79, G.80, T.81, G.82, K.83, T.84, A.85, A.327, N.329, Y.362, I.370, L.399, R.400 Chain B: R.357 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.25, A:G.77, A:G.80, A:T.81, A:G.82, A:K.83, A:K.83, A:T.84, A:Y.362, A:Y.362, A:R.400, A:R.400, B:R.357 Salt bridges: A:K.83, A:K.83 ADP.2: 17 residues within 4Å: Chain B: H.18, H.20, L.39, V.40, P.71, P.72, G.73, T.74, G.75, K.76, T.77, A.78, N.332, Y.366, I.374, L.403, R.404 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:H.20, B:V.40, B:V.40, B:G.73, B:T.74, B:G.75, B:K.76, B:T.77, B:T.77, B:T.77, B:A.78, B:N.332, B:N.332, B:Y.366 Salt bridges: B:H.18, B:K.76, B:R.404 ADP.3: 19 residues within 4Å: Chain C: A.24, H.25, H.27, I.28, M.46, V.47, G.48, P.79, G.80, T.81, G.82, K.83, T.84, A.85, Y.362, I.370, L.399, R.400 Chain D: R.357 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:H.27, C:V.47, C:G.80, C:T.81, C:G.82, C:K.83, C:T.84, C:T.84, C:T.84, C:A.85, C:E.300, C:Y.362 Salt bridges: C:K.83, C:K.83, C:R.400, C:R.400, D:R.357 ADP.4: 20 residues within 4Å: Chain D: S.17, H.18, H.20, L.39, V.40, Q.42, P.71, P.72, G.73, T.74, G.75, K.76, T.77, A.78, T.363, M.364, Y.366, I.374, L.403, R.404 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:G.73, D:G.75, D:K.76, D:T.77, D:T.363, D:Y.366, E:E.317 Salt bridges: D:H.18, D:H.18 pi-Stacking: D:Y.366 ADP.5: 21 residues within 4Å: Chain E: A.24, H.25, H.27, I.28, G.45, M.46, V.47, Q.78, P.79, G.80, T.81, G.82, K.83, T.84, A.85, Y.362, I.370, R.374, L.399, R.400 Chain L: R.357 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:A.24, E:H.27, E:V.47, E:Q.78, E:G.80, E:T.81, E:G.82, E:K.83, E:T.84, E:T.84, E:T.84, E:A.85, E:Y.362, E:Y.362 Salt bridges: E:K.83, E:R.400 ADP.6: 20 residues within 4Å: Chain A: E.317, R.353 Chain L: H.18, H.20, G.38, L.39, V.40, G.41, P.71, P.72, G.73, T.74, G.75, K.76, T.77, A.78, Y.366, E.370, I.374, R.404 18 PLIP interactions: 15 interactions with chain L, 3 interactions with chain A Hydrogen bonds: L:H.18, L:H.20, L:V.40, L:P.71, L:G.73, L:T.74, L:G.75, L:K.76, L:T.77, L:T.77, L:T.77, L:A.78, A:E.317 Salt bridges: L:H.18, L:K.76, L:R.404, A:R.353, A:R.353

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Z. et al., Structural insights into the human NuA4/TIP60 acetyltransferase and chromatin remodeling complex. Science (2024)

Release Date

2024-08-21

Peptides

RuvB-like 2: ACE
RuvB-like 1: BDL
E1A-binding protein p400: F
Enhancer of polycomb homolog 1: G
DNA methyltransferase 1-associated protein 1: H
Actin, cytoplasmic 1: I
Vacuolar protein sorting-associated protein 72 homolog: J
Actin-like protein 6A: KO
Histone H2A.Z: M
Histone H2B type 1-B: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

C
D

E
F

B
C

D
E

L
A

F
G

G
H

H
I

I
J

J
K

K
L

O
M

M
N

N
O

RuvB-like 2

RuvB-like 1

E1A-binding protein p400

Enhancer of polycomb homolog 1

DNA methyltransferase 1-associated protein 1

Actin, cytoplasmic 1

Vacuolar protein sorting-associated protein 72 homolog

Actin-like protein 6A

Histone H2A.Z

Histone H2B type 1-B

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