SMTL ID : 5trl.1

Crystal structure of human GCN5 histone acetyltransferase domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-24-mer

Ligands

24 x SCA: SUCCINYL-COENZYME A(Non-covalent)

SCA.1: 24 residues within 4Å: Chain A: Q.36, L.37, M.40, V.83, F.84, C.85, A.86, V.87, Q.92, V.93, K.94, G.95, Y.96, G.97, T.98, T.118, Y.119, Y.123, A.124, G.126, Y.127, F.128, K.130, Y.151 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:L.37, A:Y.127 Hydrogen bonds: A:C.85, A:C.85, A:V.87, A:Q.92, A:V.93, A:K.94, A:G.95, A:G.95, A:Y.96, A:G.97, A:T.98, A:Y.123 Water bridges: A:Y.119, A:Q.131, A:Q.131, A:Y.151 Salt bridges: A:K.130 SCA.2: 25 residues within 4Å: Chain B: Q.36, L.37, M.40, I.82, V.83, F.84, C.85, A.86, V.87, Q.92, V.93, K.94, G.95, Y.96, G.97, T.98, T.118, Y.119, Y.123, A.124, G.126, Y.127, F.128, K.130, Y.151 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:Q.36, B:L.37, B:Y.127 Hydrogen bonds: B:C.85, B:C.85, B:V.87, B:Q.92, B:V.93, B:K.94, B:G.95, B:Y.96, B:G.97, B:T.98, B:T.98, B:Y.123, B:K.130 Water bridges: B:Y.119 SCA.3: 25 residues within 4Å: Chain C: Q.36, L.37, I.82, V.83, F.84, C.85, A.86, V.87, Q.92, V.93, K.94, G.95, Y.96, G.97, T.98, T.118, Y.119, A.120, D.121, Y.123, A.124, G.126, Y.127, F.128, K.130 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:Q.36, C:L.37 Hydrogen bonds: C:C.85, C:C.85, C:V.87, C:Q.92, C:V.93, C:K.94, C:G.95, C:Y.96, C:G.97, C:T.98, C:T.118, C:T.118, C:D.121, C:Y.123 Salt bridges: C:K.130 SCA.4: 22 residues within 4Å: Chain D: Q.36, L.37, V.83, F.84, C.85, A.86, V.87, Q.92, V.93, K.94, G.95, Y.96, G.97, T.98, Y.119, D.121, Y.123, A.124, G.126, Y.127, K.130, Y.151 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:Q.36, D:L.37, D:Y.127 Hydrogen bonds: D:C.85, D:C.85, D:V.87, D:Q.92, D:V.93, D:K.94, D:G.95, D:Y.96, D:G.97, D:T.98, D:T.98, D:D.121, D:D.121, D:Y.123, D:K.130 Water bridges: D:Y.119, D:G.126, D:G.126 Salt bridges: D:K.130 SCA.5: 22 residues within 4Å: Chain E: Q.36, L.37, V.83, F.84, C.85, A.86, V.87, Q.92, V.93, K.94, G.95, Y.96, G.97, T.98, Y.119, A.120, D.121, Y.123, A.124, G.126, Y.127, K.130 19 PLIP interactions: 19 interactions with chain E Hydrophobic interactions: E:Q.36, E:Y.127 Hydrogen bonds: E:C.85, E:V.87, E:Q.92, E:V.93, E:K.94, E:G.95, E:G.95, E:Y.96, E:G.97, E:T.98, E:T.98, E:D.121, E:Y.123 Water bridges: E:C.85, E:T.118, E:G.126 Salt bridges: E:K.130 SCA.6: 25 residues within 4Å: Chain F: Q.36, L.37, M.40, V.83, F.84, C.85, A.86, V.87, Q.92, V.93, K.94, G.95, Y.96, G.97, T.98, T.118, Y.119, A.120, D.121, Y.123, A.124, G.126, Y.127, F.128, K.130 21 PLIP interactions: 21 interactions with chain F Hydrophobic interactions: F:Q.36, F:L.37, F:Y.127 Hydrogen bonds: F:C.85, F:C.85, F:V.87, F:Q.92, F:V.93, F:K.94, F:G.95, F:Y.96, F:G.97, F:T.98, F:T.118, F:D.121, F:Y.123, F:Y.127 Water bridges: F:Q.92, F:T.118, F:I.125 Salt bridges: F:K.130 SCA.7: 22 residues within 4Å: Chain G: Q.36, L.37, I.82, V.83, C.85, A.86, V.87, Q.92, V.93, K.94, G.95, Y.96, G.97, T.98, T.118, Y.119, Y.123, A.124, G.126, Y.127, F.128, K.130 17 PLIP interactions: 17 interactions with chain G Hydrophobic interactions: G:L.37 Hydrogen bonds: G:C.85, G:C.85, G:V.87, G:Q.92, G:V.93, G:K.94, G:G.95, G:G.95, G:Y.96, G:G.97, G:T.98, G:D.121, G:D.121, G:Y.123 Water bridges: G:G.126 Salt bridges: G:K.130 SCA.8: 25 residues within 4Å: Chain H: Q.36, L.37, M.40, I.82, V.83, F.84, C.85, A.86, V.87, Q.92, V.93, K.94, G.95, Y.96, G.97, T.98, T.118, Y.119, Y.123, A.124, G.126, Y.127, F.128, K.130, Y.151 17 PLIP interactions: 17 interactions with chain H Hydrophobic interactions: H:Q.36, H:L.37, H:Y.127 Hydrogen bonds: H:C.85, H:C.85, H:V.87, H:Q.92, H:V.93, H:K.94, H:G.95, H:Y.96, H:G.97, H:T.98, H:T.98, H:Y.123 Water bridges: H:Y.119 Salt bridges: H:K.130 SCA.9: 24 residues within 4Å: Chain I: Q.36, L.37, M.40, V.83, F.84, C.85, A.86, V.87, Q.92, V.93, K.94, G.95, Y.96, G.97, T.98, T.118, Y.119, Y.123, A.124, G.126, Y.127, F.128, K.130, Y.151 19 PLIP interactions: 19 interactions with chain I Hydrophobic interactions: I:L.37, I:Y.127 Hydrogen bonds: I:C.85, I:C.85, I:V.87, I:Q.92, I:V.93, I:K.94, I:G.95, I:G.95, I:Y.96, I:G.97, I:T.98, I:T.98, I:Y.123 Water bridges: I:Y.119, I:Q.131, I:Q.131 Salt bridges: I:K.130 SCA.10: 25 residues within 4Å: Chain J: Q.36, L.37, M.40, I.82, V.83, F.84, C.85, A.86, V.87, Q.92, V.93, K.94, G.95, Y.96, G.97, T.98, T.118, Y.119, Y.123, A.124, G.126, Y.127, F.128, K.130, Y.151 18 PLIP interactions: 18 interactions with chain J Hydrophobic interactions: J:Q.36, J:L.37, J:Y.127 Hydrogen bonds: J:C.85, J:C.85, J:V.87, J:Q.92, J:V.93, J:K.94, J:G.95, J:Y.96, J:G.97, J:T.98, J:T.98, J:T.118, J:Y.123, J:K.130 Water bridges: J:Y.119 SCA.11: 25 residues within 4Å: Chain K: Q.36, L.37, I.82, V.83, F.84, C.85, A.86, V.87, Q.92, V.93, K.94, G.95, Y.96, G.97, T.98, T.118, Y.119, A.120, D.121, Y.123, A.124, G.126, Y.127, F.128, K.130 17 PLIP interactions: 17 interactions with chain K Hydrophobic interactions: K:Q.36, K:L.37 Hydrogen bonds: K:C.85, K:C.85, K:V.87, K:Q.92, K:V.93, K:K.94, K:G.95, K:Y.96, K:G.97, K:T.98, K:T.118, K:T.118, K:D.121, K:Y.123 Salt bridges: K:K.130 SCA.12: 22 residues within 4Å: Chain L: Q.36, L.37, V.83, F.84, C.85, A.86, V.87, Q.92, V.93, K.94, G.95, Y.96, G.97, T.98, Y.119, D.121, Y.123, A.124, G.126, Y.127, K.130, Y.151 22 PLIP interactions: 22 interactions with chain L Hydrophobic interactions: L:Q.36, L:L.37, L:Y.127 Hydrogen bonds: L:C.85, L:C.85, L:V.87, L:Q.92, L:V.93, L:K.94, L:G.95, L:Y.96, L:G.97, L:T.98, L:D.121, L:D.121, L:Y.123, L:K.130 Water bridges: L:T.98, L:Y.119, L:G.126, L:G.126 Salt bridges: L:K.130 SCA.13: 22 residues within 4Å: Chain M: Q.36, L.37, V.83, F.84, C.85, A.86, V.87, Q.92, V.93, K.94, G.95, Y.96, G.97, T.98, Y.119, A.120, D.121, Y.123, A.124, G.126, Y.127, K.130 18 PLIP interactions: 18 interactions with chain M Hydrophobic interactions: M:Q.36, M:Y.127 Hydrogen bonds: M:C.85, M:V.87, M:Q.92, M:V.93, M:K.94, M:G.95, M:G.95, M:Y.96, M:G.97, M:T.98, M:D.121, M:Y.123 Water bridges: M:C.85, M:T.118, M:G.126 Salt bridges: M:K.130 SCA.14: 25 residues within 4Å: Chain N: Q.36, L.37, M.40, V.83, F.84, C.85, A.86, V.87, Q.92, V.93, K.94, G.95, Y.96, G.97, T.98, T.118, Y.119, A.120, D.121, Y.123, A.124, G.126, Y.127, F.128, K.130 20 PLIP interactions: 20 interactions with chain N Hydrophobic interactions: N:Q.36, N:L.37, N:Y.127 Hydrogen bonds: N:C.85, N:C.85, N:V.87, N:Q.92, N:V.93, N:K.94, N:G.95, N:Y.96, N:G.97, N:T.98, N:T.118, N:D.121, N:Y.123, N:Y.127 Water bridges: N:Q.92, N:I.125 Salt bridges: N:K.130 SCA.15: 22 residues within 4Å: Chain O: Q.36, L.37, I.82, V.83, C.85, A.86, V.87, Q.92, V.93, K.94, G.95, Y.96, G.97, T.98, T.118, Y.119, Y.123, A.124, G.126, Y.127, F.128, K.130 18 PLIP interactions: 18 interactions with chain O Hydrophobic interactions: O:L.37 Hydrogen bonds: O:C.85, O:C.85, O:V.87, O:Q.92, O:V.93, O:K.94, O:G.95, O:G.95, O:Y.96, O:G.97, O:T.98, O:T.118, O:D.121, O:D.121, O:Y.123 Water bridges: O:G.126 Salt bridges: O:K.130 SCA.16: 25 residues within 4Å: Chain P: Q.36, L.37, M.40, I.82, V.83, F.84, C.85, A.86, V.87, Q.92, V.93, K.94, G.95, Y.96, G.97, T.98, T.118, Y.119, Y.123, A.124, G.126, Y.127, F.128, K.130, Y.151 16 PLIP interactions: 16 interactions with chain P Hydrophobic interactions: P:Q.36, P:L.37, P:Y.127 Hydrogen bonds: P:C.85, P:C.85, P:V.87, P:Q.92, P:V.93, P:K.94, P:G.95, P:Y.96, P:G.97, P:T.98, P:Y.123 Water bridges: P:Y.119 Salt bridges: P:K.130 SCA.17: 24 residues within 4Å: Chain Q: Q.36, L.37, M.40, V.83, F.84, C.85, A.86, V.87, Q.92, V.93, K.94, G.95, Y.96, G.97, T.98, T.118, Y.119, Y.123, A.124, G.126, Y.127, F.128, K.130, Y.151 20 PLIP interactions: 20 interactions with chain Q Hydrophobic interactions: Q:L.37, Q:Y.127 Hydrogen bonds: Q:C.85, Q:C.85, Q:V.87, Q:Q.92, Q:V.93, Q:K.94, Q:G.95, Q:G.95, Q:Y.96, Q:G.97, Q:T.98, Q:T.98, Q:Y.123 Water bridges: Q:Y.119, Q:Q.131, Q:Q.131, Q:Y.151 Salt bridges: Q:K.130 SCA.18: 25 residues within 4Å: Chain R: Q.36, L.37, M.40, I.82, V.83, F.84, C.85, A.86, V.87, Q.92, V.93, K.94, G.95, Y.96, G.97, T.98, T.118, Y.119, Y.123, A.124, G.126, Y.127, F.128, K.130, Y.151 17 PLIP interactions: 17 interactions with chain R Hydrophobic interactions: R:Q.36, R:L.37, R:Y.127 Hydrogen bonds: R:C.85, R:C.85, R:V.87, R:Q.92, R:V.93, R:K.94, R:G.95, R:Y.96, R:G.97, R:T.98, R:T.98, R:Y.123, R:K.130 Water bridges: R:Y.119 SCA.19: 25 residues within 4Å: Chain S: Q.36, L.37, I.82, V.83, F.84, C.85, A.86, V.87, Q.92, V.93, K.94, G.95, Y.96, G.97, T.98, T.118, Y.119, A.120, D.121, Y.123, A.124, G.126, Y.127, F.128, K.130 16 PLIP interactions: 16 interactions with chain S Hydrophobic interactions: S:Q.36, S:L.37 Hydrogen bonds: S:C.85, S:C.85, S:V.87, S:Q.92, S:V.93, S:K.94, S:G.95, S:Y.96, S:G.97, S:T.98, S:T.118, S:D.121, S:Y.123 Salt bridges: S:K.130 SCA.20: 22 residues within 4Å: Chain T: Q.36, L.37, V.83, F.84, C.85, A.86, V.87, Q.92, V.93, K.94, G.95, Y.96, G.97, T.98, Y.119, D.121, Y.123, A.124, G.126, Y.127, K.130, Y.151 22 PLIP interactions: 22 interactions with chain T Hydrophobic interactions: T:Q.36, T:L.37, T:Y.127 Hydrogen bonds: T:C.85, T:C.85, T:V.87, T:Q.92, T:V.93, T:K.94, T:G.95, T:Y.96, T:G.97, T:T.98, T:D.121, T:D.121, T:Y.123, T:K.130 Water bridges: T:T.98, T:Y.119, T:G.126, T:G.126 Salt bridges: T:K.130 SCA.21: 22 residues within 4Å: Chain U: Q.36, L.37, V.83, F.84, C.85, A.86, V.87, Q.92, V.93, K.94, G.95, Y.96, G.97, T.98, Y.119, A.120, D.121, Y.123, A.124, G.126, Y.127, K.130 19 PLIP interactions: 19 interactions with chain U Hydrophobic interactions: U:Q.36, U:Y.127 Hydrogen bonds: U:C.85, U:V.87, U:Q.92, U:V.93, U:K.94, U:G.95, U:G.95, U:Y.96, U:G.97, U:T.98, U:T.98, U:D.121, U:Y.123 Water bridges: U:C.85, U:T.118, U:G.126 Salt bridges: U:K.130 SCA.22: 25 residues within 4Å: Chain V: Q.36, L.37, M.40, V.83, F.84, C.85, A.86, V.87, Q.92, V.93, K.94, G.95, Y.96, G.97, T.98, T.118, Y.119, A.120, D.121, Y.123, A.124, G.126, Y.127, F.128, K.130 21 PLIP interactions: 21 interactions with chain V Hydrophobic interactions: V:Q.36, V:L.37, V:Y.127 Hydrogen bonds: V:C.85, V:C.85, V:V.87, V:Q.92, V:V.93, V:K.94, V:G.95, V:Y.96, V:G.97, V:T.98, V:T.98, V:T.118, V:D.121, V:Y.123, V:Y.127 Water bridges: V:Q.92, V:I.125 Salt bridges: V:K.130 SCA.23: 22 residues within 4Å: Chain W: Q.36, L.37, I.82, V.83, C.85, A.86, V.87, Q.92, V.93, K.94, G.95, Y.96, G.97, T.98, T.118, Y.119, Y.123, A.124, G.126, Y.127, F.128, K.130 17 PLIP interactions: 17 interactions with chain W Hydrophobic interactions: W:L.37 Hydrogen bonds: W:C.85, W:C.85, W:V.87, W:Q.92, W:V.93, W:K.94, W:G.95, W:G.95, W:Y.96, W:G.97, W:T.98, W:T.98, W:D.121, W:Y.123 Water bridges: W:G.126 Salt bridges: W:K.130 SCA.24: 25 residues within 4Å: Chain X: Q.36, L.37, M.40, I.82, V.83, F.84, C.85, A.86, V.87, Q.92, V.93, K.94, G.95, Y.96, G.97, T.98, T.118, Y.119, Y.123, A.124, G.126, Y.127, F.128, K.130, Y.151 17 PLIP interactions: 17 interactions with chain X Hydrophobic interactions: X:Q.36, X:L.37, X:Y.127 Hydrogen bonds: X:C.85, X:C.85, X:V.87, X:Q.92, X:V.93, X:K.94, X:G.95, X:Y.96, X:G.97, X:T.98, X:T.98, X:Y.123 Water bridges: X:Y.119 Salt bridges: X:K.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y. et al., KAT2A coupled with the alpha-KGDH complex acts as a histone H3 succinyltransferase. Nature (2017)

Release Date

2017-12-06

Peptides

Histone acetyltransferase KAT2A: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

D
F

E
B

F
A

G
G

H
H

I
C

J
D

K
E

L
F

M
B

N
A

O
G

P
H

Q
C

R
D

S
E

T
F

U
B

V
A

W
G

X
H

Histone acetyltransferase KAT2A

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