SMTL ID : 8e6o.1

Crystal structure of human GCN5 histone acetyltransferase domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

homo-24-mer

Ligands

24 x UQ3: S-{(3S,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5,10,14-tetraoxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (2R)-2-hydroxypropanethioate(Non-covalent)(Covalent)

UQ3.1: 23 residues within 4Å: Chain A: Q.33, L.34, I.79, V.80, F.81, C.82, A.83, V.84, Q.89, V.90, K.91, G.92, Y.93, G.94, T.95, T.115, Y.116, Y.120, A.121, G.123, Y.124, F.125, K.127 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:Q.33, A:L.34, A:Y.124 Hydrogen bonds: A:C.82, A:C.82, A:V.84, A:Q.89, A:V.90, A:G.92, A:Y.93, A:G.94, A:T.95, A:T.95, A:T.115, A:Y.116, A:Y.120, A:Y.124 Water bridges: A:Q.89, A:K.91, A:G.123 Salt bridges: A:K.127 UQ3.2: 22 residues within 4Å: Chain B: Q.33, L.34, M.37, V.80, F.81, C.82, A.83, V.84, Q.89, V.90, K.91, G.92, Y.93, G.94, T.95, T.115, Y.116, Y.120, G.123, Y.124, F.125, K.127 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.34 Hydrogen bonds: B:V.84, B:Q.89, B:V.90, B:K.91, B:G.92, B:Y.93, B:G.94, B:T.95, B:Y.120 Water bridges: B:Y.116, B:Y.116, B:Y.116, B:D.118 Salt bridges: B:K.127, B:K.127 UQ3.3: 23 residues within 4Å: Chain C: Q.33, L.34, I.79, V.80, F.81, C.82, A.83, V.84, Q.89, V.90, K.91, G.92, Y.93, G.94, T.95, T.115, Y.116, Y.120, A.121, G.123, Y.124, F.125, K.127 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:Q.33, C:L.34, C:Y.124, C:F.125 Hydrogen bonds: C:C.82, C:C.82, C:V.84, C:Q.89, C:V.90, C:K.91, C:G.92, C:Y.93, C:G.94, C:T.95, C:Y.116, C:Y.120, C:K.127 Water bridges: C:Y.116 Salt bridges: C:K.127 UQ3.4: 23 residues within 4Å: Chain D: Q.33, L.34, I.79, V.80, F.81, C.82, A.83, V.84, Q.89, V.90, K.91, G.92, Y.93, G.94, T.95, T.115, Y.116, Y.120, A.121, G.123, Y.124, F.125, K.127 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:Q.33, D:L.34, D:Y.124 Hydrogen bonds: D:C.82, D:C.82, D:V.84, D:Q.89, D:V.90, D:G.92, D:Y.93, D:G.94, D:T.95, D:T.95, D:T.115, D:Y.116, D:Y.120, D:Y.124 Water bridges: D:Q.89, D:K.91, D:G.123 Salt bridges: D:K.127 UQ3.5: 22 residues within 4Å: Chain E: Q.33, L.34, M.37, V.80, F.81, C.82, A.83, V.84, Q.89, V.90, K.91, G.92, Y.93, G.94, T.95, T.115, Y.116, Y.120, G.123, Y.124, F.125, K.127 16 PLIP interactions: 16 interactions with chain E Hydrophobic interactions: E:L.34 Hydrogen bonds: E:V.84, E:Q.89, E:V.90, E:K.91, E:G.92, E:Y.93, E:G.94, E:T.95, E:Y.120 Water bridges: E:Y.116, E:Y.116, E:Y.116, E:D.118 Salt bridges: E:K.127, E:K.127 UQ3.6: 23 residues within 4Å: Chain F: Q.33, L.34, I.79, V.80, F.81, C.82, A.83, V.84, Q.89, V.90, K.91, G.92, Y.93, G.94, T.95, T.115, Y.116, Y.120, A.121, G.123, Y.124, F.125, K.127 19 PLIP interactions: 19 interactions with chain F Hydrophobic interactions: F:Q.33, F:L.34, F:Y.124, F:F.125 Hydrogen bonds: F:C.82, F:C.82, F:V.84, F:Q.89, F:V.90, F:K.91, F:G.92, F:Y.93, F:G.94, F:T.95, F:Y.116, F:Y.120, F:K.127 Water bridges: F:Y.116 Salt bridges: F:K.127 UQ3.7: 23 residues within 4Å: Chain G: Q.33, L.34, I.79, V.80, F.81, C.82, A.83, V.84, Q.89, V.90, K.91, G.92, Y.93, G.94, T.95, T.115, Y.116, Y.120, A.121, G.123, Y.124, F.125, K.127 21 PLIP interactions: 21 interactions with chain G Hydrophobic interactions: G:Q.33, G:L.34, G:Y.124 Hydrogen bonds: G:C.82, G:C.82, G:V.84, G:Q.89, G:V.90, G:G.92, G:Y.93, G:G.94, G:T.95, G:T.95, G:T.115, G:Y.116, G:Y.120, G:Y.124 Water bridges: G:Q.89, G:K.91, G:G.123 Salt bridges: G:K.127 UQ3.8: 22 residues within 4Å: Chain H: Q.33, L.34, M.37, V.80, F.81, C.82, A.83, V.84, Q.89, V.90, K.91, G.92, Y.93, G.94, T.95, T.115, Y.116, Y.120, G.123, Y.124, F.125, K.127 16 PLIP interactions: 16 interactions with chain H Hydrophobic interactions: H:L.34 Hydrogen bonds: H:V.84, H:Q.89, H:V.90, H:K.91, H:G.92, H:Y.93, H:G.94, H:T.95, H:Y.120 Water bridges: H:Y.116, H:Y.116, H:Y.116, H:D.118 Salt bridges: H:K.127, H:K.127 UQ3.9: 23 residues within 4Å: Chain I: Q.33, L.34, I.79, V.80, F.81, C.82, A.83, V.84, Q.89, V.90, K.91, G.92, Y.93, G.94, T.95, T.115, Y.116, Y.120, A.121, G.123, Y.124, F.125, K.127 19 PLIP interactions: 19 interactions with chain I Hydrophobic interactions: I:Q.33, I:L.34, I:Y.124, I:F.125 Hydrogen bonds: I:C.82, I:C.82, I:V.84, I:Q.89, I:V.90, I:K.91, I:G.92, I:Y.93, I:G.94, I:T.95, I:Y.116, I:Y.120, I:K.127 Water bridges: I:Y.116 Salt bridges: I:K.127 UQ3.10: 23 residues within 4Å: Chain J: Q.33, L.34, I.79, V.80, F.81, C.82, A.83, V.84, Q.89, V.90, K.91, G.92, Y.93, G.94, T.95, T.115, Y.116, Y.120, A.121, G.123, Y.124, F.125, K.127 21 PLIP interactions: 21 interactions with chain J Hydrophobic interactions: J:Q.33, J:L.34, J:Y.124 Hydrogen bonds: J:C.82, J:C.82, J:V.84, J:Q.89, J:V.90, J:G.92, J:Y.93, J:G.94, J:T.95, J:T.95, J:T.115, J:Y.116, J:Y.120, J:Y.124 Water bridges: J:Q.89, J:K.91, J:G.123 Salt bridges: J:K.127 UQ3.11: 22 residues within 4Å: Chain K: Q.33, L.34, M.37, V.80, F.81, C.82, A.83, V.84, Q.89, V.90, K.91, G.92, Y.93, G.94, T.95, T.115, Y.116, Y.120, G.123, Y.124, F.125, K.127 16 PLIP interactions: 16 interactions with chain K Hydrophobic interactions: K:L.34 Hydrogen bonds: K:V.84, K:Q.89, K:V.90, K:K.91, K:G.92, K:Y.93, K:G.94, K:T.95, K:Y.120 Water bridges: K:Y.116, K:Y.116, K:Y.116, K:D.118 Salt bridges: K:K.127, K:K.127 UQ3.12: 23 residues within 4Å: Chain L: Q.33, L.34, I.79, V.80, F.81, C.82, A.83, V.84, Q.89, V.90, K.91, G.92, Y.93, G.94, T.95, T.115, Y.116, Y.120, A.121, G.123, Y.124, F.125, K.127 19 PLIP interactions: 19 interactions with chain L Hydrophobic interactions: L:Q.33, L:L.34, L:Y.124, L:F.125 Hydrogen bonds: L:C.82, L:C.82, L:V.84, L:Q.89, L:V.90, L:K.91, L:G.92, L:Y.93, L:G.94, L:T.95, L:Y.116, L:Y.120, L:K.127 Water bridges: L:Y.116 Salt bridges: L:K.127 UQ3.13: 23 residues within 4Å: Chain M: Q.33, L.34, I.79, V.80, F.81, C.82, A.83, V.84, Q.89, V.90, K.91, G.92, Y.93, G.94, T.95, T.115, Y.116, Y.120, A.121, G.123, Y.124, F.125, K.127 19 PLIP interactions: 19 interactions with chain M Hydrophobic interactions: M:Q.33, M:L.34, M:Y.124 Hydrogen bonds: M:C.82, M:C.82, M:V.84, M:Q.89, M:V.90, M:G.92, M:Y.93, M:G.94, M:T.95, M:Y.116, M:Y.120, M:Y.124 Water bridges: M:Q.89, M:K.91, M:G.123 Salt bridges: M:K.127 UQ3.14: 22 residues within 4Å: Chain N: Q.33, L.34, M.37, V.80, F.81, C.82, A.83, V.84, Q.89, V.90, K.91, G.92, Y.93, G.94, T.95, T.115, Y.116, Y.120, G.123, Y.124, F.125, K.127 17 PLIP interactions: 17 interactions with chain N Hydrophobic interactions: N:L.34 Hydrogen bonds: N:V.84, N:Q.89, N:V.90, N:K.91, N:G.92, N:Y.93, N:G.94, N:T.95, N:T.95, N:Y.120 Water bridges: N:T.115, N:Y.116, N:Y.116, N:D.118 Salt bridges: N:K.127, N:K.127 UQ3.15: 23 residues within 4Å: Chain O: Q.33, L.34, I.79, V.80, F.81, C.82, A.83, V.84, Q.89, V.90, K.91, G.92, Y.93, G.94, T.95, T.115, Y.116, Y.120, A.121, G.123, Y.124, F.125, K.127 20 PLIP interactions: 20 interactions with chain O Hydrophobic interactions: O:Q.33, O:L.34, O:Y.124, O:F.125 Hydrogen bonds: O:C.82, O:C.82, O:V.84, O:Q.89, O:V.90, O:K.91, O:G.92, O:Y.93, O:G.94, O:T.95, O:T.95, O:Y.116, O:Y.120, O:K.127 Water bridges: O:Y.116 Salt bridges: O:K.127 UQ3.16: 23 residues within 4Å: Chain P: Q.33, L.34, I.79, V.80, F.81, C.82, A.83, V.84, Q.89, V.90, K.91, G.92, Y.93, G.94, T.95, T.115, Y.116, Y.120, A.121, G.123, Y.124, F.125, K.127 19 PLIP interactions: 19 interactions with chain P Hydrophobic interactions: P:Q.33, P:L.34, P:Y.124 Hydrogen bonds: P:C.82, P:C.82, P:V.84, P:Q.89, P:V.90, P:G.92, P:Y.93, P:G.94, P:T.95, P:Y.116, P:Y.120, P:Y.124 Water bridges: P:Q.89, P:K.91, P:G.123 Salt bridges: P:K.127 UQ3.17: 22 residues within 4Å: Chain Q: Q.33, L.34, M.37, V.80, F.81, C.82, A.83, V.84, Q.89, V.90, K.91, G.92, Y.93, G.94, T.95, T.115, Y.116, Y.120, G.123, Y.124, F.125, K.127 17 PLIP interactions: 17 interactions with chain Q Hydrophobic interactions: Q:L.34 Hydrogen bonds: Q:V.84, Q:Q.89, Q:V.90, Q:K.91, Q:G.92, Q:Y.93, Q:G.94, Q:T.95, Q:T.95, Q:Y.120 Water bridges: Q:T.115, Q:Y.116, Q:Y.116, Q:D.118 Salt bridges: Q:K.127, Q:K.127 UQ3.18: 23 residues within 4Å: Chain R: Q.33, L.34, I.79, V.80, F.81, C.82, A.83, V.84, Q.89, V.90, K.91, G.92, Y.93, G.94, T.95, T.115, Y.116, Y.120, A.121, G.123, Y.124, F.125, K.127 20 PLIP interactions: 20 interactions with chain R Hydrophobic interactions: R:Q.33, R:L.34, R:Y.124, R:F.125 Hydrogen bonds: R:C.82, R:C.82, R:V.84, R:Q.89, R:V.90, R:K.91, R:G.92, R:Y.93, R:G.94, R:T.95, R:T.95, R:Y.116, R:Y.120, R:K.127 Water bridges: R:Y.116 Salt bridges: R:K.127 UQ3.19: 23 residues within 4Å: Chain S: Q.33, L.34, I.79, V.80, F.81, C.82, A.83, V.84, Q.89, V.90, K.91, G.92, Y.93, G.94, T.95, T.115, Y.116, Y.120, A.121, G.123, Y.124, F.125, K.127 19 PLIP interactions: 19 interactions with chain S Hydrophobic interactions: S:Q.33, S:L.34, S:Y.124 Hydrogen bonds: S:C.82, S:C.82, S:V.84, S:Q.89, S:V.90, S:G.92, S:Y.93, S:G.94, S:T.95, S:Y.116, S:Y.120, S:Y.124 Water bridges: S:Q.89, S:K.91, S:G.123 Salt bridges: S:K.127 UQ3.20: 22 residues within 4Å: Chain T: Q.33, L.34, M.37, V.80, F.81, C.82, A.83, V.84, Q.89, V.90, K.91, G.92, Y.93, G.94, T.95, T.115, Y.116, Y.120, G.123, Y.124, F.125, K.127 17 PLIP interactions: 17 interactions with chain T Hydrophobic interactions: T:L.34 Hydrogen bonds: T:V.84, T:Q.89, T:V.90, T:K.91, T:G.92, T:Y.93, T:G.94, T:T.95, T:T.95, T:Y.120 Water bridges: T:T.115, T:Y.116, T:Y.116, T:D.118 Salt bridges: T:K.127, T:K.127 UQ3.21: 23 residues within 4Å: Chain U: Q.33, L.34, I.79, V.80, F.81, C.82, A.83, V.84, Q.89, V.90, K.91, G.92, Y.93, G.94, T.95, T.115, Y.116, Y.120, A.121, G.123, Y.124, F.125, K.127 20 PLIP interactions: 20 interactions with chain U Hydrophobic interactions: U:Q.33, U:L.34, U:Y.124, U:F.125 Hydrogen bonds: U:C.82, U:C.82, U:V.84, U:Q.89, U:V.90, U:K.91, U:G.92, U:Y.93, U:G.94, U:T.95, U:T.95, U:Y.116, U:Y.120, U:K.127 Water bridges: U:Y.116 Salt bridges: U:K.127 UQ3.22: 23 residues within 4Å: Chain V: Q.33, L.34, I.79, V.80, F.81, C.82, A.83, V.84, Q.89, V.90, K.91, G.92, Y.93, G.94, T.95, T.115, Y.116, Y.120, A.121, G.123, Y.124, F.125, K.127 19 PLIP interactions: 19 interactions with chain V Hydrophobic interactions: V:Q.33, V:L.34, V:Y.124 Hydrogen bonds: V:C.82, V:C.82, V:V.84, V:Q.89, V:V.90, V:G.92, V:Y.93, V:G.94, V:T.95, V:Y.116, V:Y.120, V:Y.124 Water bridges: V:Q.89, V:K.91, V:G.123 Salt bridges: V:K.127 UQ3.23: 22 residues within 4Å: Chain W: Q.33, L.34, M.37, V.80, F.81, C.82, A.83, V.84, Q.89, V.90, K.91, G.92, Y.93, G.94, T.95, T.115, Y.116, Y.120, G.123, Y.124, F.125, K.127 17 PLIP interactions: 17 interactions with chain W Hydrophobic interactions: W:L.34 Hydrogen bonds: W:V.84, W:Q.89, W:V.90, W:K.91, W:G.92, W:Y.93, W:G.94, W:T.95, W:T.95, W:Y.120 Water bridges: W:T.115, W:Y.116, W:Y.116, W:D.118 Salt bridges: W:K.127, W:K.127 UQ3.24: 23 residues within 4Å: Chain X: Q.33, L.34, I.79, V.80, F.81, C.82, A.83, V.84, Q.89, V.90, K.91, G.92, Y.93, G.94, T.95, T.115, Y.116, Y.120, A.121, G.123, Y.124, F.125, K.127 20 PLIP interactions: 20 interactions with chain X Hydrophobic interactions: X:Q.33, X:L.34, X:Y.124, X:F.125 Hydrogen bonds: X:C.82, X:C.82, X:V.84, X:Q.89, X:V.90, X:K.91, X:G.92, X:Y.93, X:G.94, X:T.95, X:T.95, X:Y.116, X:Y.120, X:K.127 Water bridges: X:Y.116 Salt bridges: X:K.127

Links

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Citation

Zhu, R. et al., ACSS2 acts as a lactyl-CoA synthetase and couples KAT2A to function as a lactyltransferase for histone lactylation and tumor immune evasion. Cell Metab. (2025)

Release Date

2024-02-28

Peptides

Histone acetyltransferase KAT2A: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

G
A

H
B

I
C

J
A

K
B

L
C

M
A

N
B

O
C

P
A

Q
B

R
C

S
A

T
B

U
C

V
A

W
B

X
C

Histone acetyltransferase KAT2A