SMTL ID : 8xvg.1

Structure of human NuA4/TIP60 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 12 residues within 4Å: Chain A: K.3017, R.3020, K.3021, R.3051, Q.3052, K.3055, K.3125, K.3165, K.3168, K.3529, N.3734, F.3735 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:R.3020, A:R.3051, A:R.3051 Salt bridges: A:K.3017, A:R.3020, A:K.3021, A:K.3021, A:K.3021, A:R.3051, A:K.3055, A:K.3055, A:K.3055, A:K.3125, A:K.3125, A:K.3165, A:K.3165, A:K.3165, A:K.3168, A:K.3529, A:K.3529

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

ADP.2: 21 residues within 4Å: Chain B: S.17, H.18, H.20, G.38, L.39, V.40, G.41, P.72, G.73, T.74, G.75, K.76, T.77, A.78, N.332, Y.366, I.374, R.404 Chain C: R.314, E.317, R.353 23 PLIP interactions: 19 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:S.17, B:S.17, B:V.40, B:G.41, B:G.73, B:T.74, B:T.74, B:G.75, B:K.76, B:T.77, B:T.77, B:A.78, B:N.332, B:Y.366, B:R.378, B:R.404, B:R.404 Salt bridges: B:H.18, B:K.76, C:R.314, C:R.314, C:R.353, C:R.353 ADP.3: 22 residues within 4Å: Chain C: A.24, H.25, H.27, G.45, M.46, V.47, G.48, P.79, G.80, T.81, G.82, K.83, T.84, A.85, N.329, Y.362, I.370, R.374, L.399, R.400 Chain D: E.320, R.357 21 PLIP interactions: 20 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:H.25, C:V.47, C:G.48, C:G.80, C:G.82, C:K.83, C:T.84, C:T.84, C:T.84, C:T.84, C:A.85, C:N.329, C:N.329, C:Y.362, C:Y.362, C:R.374 Salt bridges: C:H.25, C:K.83, C:R.400, C:R.400, D:R.357 ADP.4: 16 residues within 4Å: Chain D: S.17, H.18, H.20, G.38, L.39, V.40, P.71, G.73, T.74, G.75, K.76, T.77, A.78, Y.366, I.374, R.404 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:S.17, D:S.17, D:V.40, D:G.41, D:G.73, D:T.74, D:G.75, D:K.76, D:T.77, D:T.77, D:A.78, D:Y.366 Salt bridges: D:H.18, D:K.76 ADP.5: 16 residues within 4Å: Chain E: A.24, H.25, H.27, V.47, Q.78, G.80, T.81, G.82, K.83, T.84, A.85, Y.362, I.370, L.399, R.400, I.403 17 PLIP interactions: 1 interactions with chain F, 16 interactions with chain E Hydrogen bonds: F:R.357, E:A.24, 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, E:R.400 Salt bridges: E:H.25, E:K.83, E:R.400 ADP.6: 17 residues within 4Å: Chain F: S.17, H.18, H.20, G.38, L.39, V.40, G.73, T.74, G.75, K.76, T.77, A.78, Y.366, I.374, R.378, R.404 Chain G: R.353 18 PLIP interactions: 15 interactions with chain F, 3 interactions with chain G Hydrogen bonds: F:S.17, F:H.20, F:V.40, F:G.73, F:T.74, F:G.75, F:K.76, F:T.77, F:A.78, F:Y.366, F:Y.366, G:R.353, G:R.353 Salt bridges: F:H.18, F:K.76, F:R.404, F:R.404, G:R.353 ADP.7: 22 residues within 4Å: Chain B: E.320 Chain G: A.24, H.25, H.27, G.45, M.46, V.47, G.48, 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, I.403 16 PLIP interactions: 15 interactions with chain G, 1 interactions with chain B Hydrogen bonds: G:A.24, G:V.47, G:G.80, G:T.81, G:G.82, G:K.83, G:T.84, G:T.84, G:A.85, G:N.329, G:Y.362, B:E.320 Salt bridges: G:H.25, G:K.83, G:R.400, G:R.400 ADP.8: 16 residues within 4Å: Chain J: S.20, Y.21, T.22, R.24, D.171, G.173, A.174, T.175, H.176, Q.260, Q.263, A.264, G.353, N.354, L.356, R.390 9 PLIP interactions: 9 interactions with chain J Hydrogen bonds: J:S.20, J:S.20, J:Y.21, J:T.22, J:A.174, J:Q.263, J:A.264, J:G.353, J:R.390 ADP.9: 16 residues within 4Å: Chain K: S.20, Y.21, T.22, R.24, G.91, D.171, G.173, A.174, H.176, Q.260, A.264, G.353, N.354, L.356, I.357, R.390 10 PLIP interactions: 10 interactions with chain K Hydrogen bonds: K:S.20, K:Y.21, K:T.22, K:T.22, K:R.24, K:R.24, K:A.174, K:G.353, K:N.354, K:R.390 ADP.10: 16 residues within 4Å: Chain L: D.11, G.13, S.14, M.16, K.18, D.154, G.156, D.157, G.182, R.210, K.213, E.214, G.302, T.303, M.305, K.336 10 PLIP interactions: 10 interactions with chain L Hydrogen bonds: L:D.11, L:S.14, L:D.157, L:D.157, L:R.210, L:K.213, L:G.302, L:T.303 Salt bridges: L:K.18, L:K.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, K. et al., Structure of the human TIP60 complex. Nat Commun (2024)

Release Date

2024-07-24

Peptides

Isoform 2 of Transformation/transcription domain-associated protein: A
RuvB-like 1: BDF
RuvB-like 2: CEG
DNA methyltransferase 1-associated protein 1: H
Isoform 2 of E1A-binding protein p400: I
Actin-like protein 6A: JK
ACTB protein (Fragment): L
Isoform 2 of Enhancer of polycomb homolog 1: M
Vacuolar protein sorting-associated protein 72 homolog: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
A

D
C

F
E

C
B

E
D

G
F

H
G

I
H

J
I

K
J

L
K

M
M

N
N

Isoform 2 of Transformation/transcription domain-associated protein

RuvB-like 1

RuvB-like 2

DNA methyltransferase 1-associated protein 1

Isoform 2 of E1A-binding protein p400

Actin-like protein 6A

ACTB protein (Fragment)

Isoform 2 of Enhancer of polycomb homolog 1

Vacuolar protein sorting-associated protein 72 homolog

Related Entries With Identical Sequence