SMTL ID : 8h6c.1

Crystal structure of human GCN5 histone acetyltransferase domain bound with malonyl-CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-octamer

Ligands

8 x MLC: MALONYL-COENZYME A(Non-covalent)

MLC.1: 22 residues within 4Å: Chain A: Q.34, L.35, M.38, V.81, F.82, C.83, A.84, V.85, Q.90, V.91, K.92, G.93, Y.94, G.95, T.96, Y.117, Y.121, A.122, G.124, Y.125, F.126, K.128 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.35, A:Y.125 Hydrogen bonds: A:C.83, A:C.83, A:V.85, A:Q.90, A:V.91, A:K.92, A:G.93, A:Y.94, A:G.95, A:T.96, A:T.96, A:T.116, A:Y.121 Water bridges: A:Q.90 Salt bridges: A:K.128 MLC.2: 24 residues within 4Å: Chain B: Q.34, L.35, M.38, I.80, V.81, F.82, C.83, A.84, V.85, Q.90, V.91, K.92, G.93, Y.94, G.95, T.96, T.116, Y.117, Y.121, A.122, G.124, Y.125, F.126, K.128 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:Q.34, B:L.35, B:Y.125 Hydrogen bonds: B:C.83, B:C.83, B:V.85, B:Q.90, B:V.91, B:K.92, B:G.93, B:Y.94, B:G.95, B:T.96, B:T.116, B:Y.117, B:Y.121, B:K.128, B:K.128 Water bridges: B:Q.90, B:Y.117, B:G.124, B:Y.125 Salt bridges: B:K.128 MLC.3: 23 residues within 4Å: Chain C: Q.34, L.35, V.81, F.82, C.83, A.84, V.85, Q.90, V.91, K.92, G.93, Y.94, G.95, T.96, T.116, Y.117, D.119, Y.121, A.122, G.124, Y.125, F.126, K.128 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:Q.34, C:L.35 Hydrogen bonds: C:C.83, C:C.83, C:V.85, C:Q.90, C:V.91, C:K.92, C:G.93, C:G.95, C:T.96, C:T.96, C:Y.121, C:K.128 Water bridges: C:Q.90, C:Y.94 Salt bridges: C:K.128 MLC.4: 23 residues within 4Å: Chain D: Q.34, L.35, V.81, F.82, C.83, A.84, V.85, Q.90, V.91, K.92, G.93, Y.94, G.95, T.96, T.116, Y.117, D.119, Y.121, A.122, G.124, Y.125, F.126, K.128 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:L.35, D:Y.125 Hydrogen bonds: D:C.83, D:C.83, D:V.85, D:Q.90, D:V.91, D:K.92, D:G.93, D:G.95, D:T.96, D:Y.121, D:K.128 Water bridges: D:Q.90, D:Y.94 Salt bridges: D:K.128 MLC.5: 22 residues within 4Å: Chain E: Q.34, L.35, V.81, F.82, C.83, A.84, V.85, Q.90, V.91, K.92, G.93, Y.94, G.95, T.96, T.116, Y.117, Y.121, A.122, G.124, Y.125, F.126, K.128 17 PLIP interactions: 17 interactions with chain E Hydrophobic interactions: E:Y.125, E:F.126 Hydrogen bonds: E:V.81, E:C.83, E:C.83, E:V.85, E:Q.90, E:V.91, E:K.92, E:G.93, E:G.95, E:T.96, E:Y.121 Water bridges: E:V.91, E:Y.94, E:Y.94 Salt bridges: E:K.128 MLC.6: 17 residues within 4Å: Chain F: Q.34, L.35, C.83, A.84, V.85, Q.90, V.91, K.92, G.93, Y.94, G.95, T.96, Y.121, A.122, G.124, Y.125, K.128 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:L.35, F:Y.125 Hydrogen bonds: F:C.83, F:V.85, F:Q.90, F:V.91, F:K.92, F:G.93, F:G.95, F:T.96, F:T.96, F:Y.121, F:K.128 Salt bridges: F:K.128 MLC.7: 23 residues within 4Å: Chain G: Q.34, L.35, I.80, V.81, F.82, C.83, A.84, V.85, Q.90, V.91, K.92, G.93, Y.94, G.95, T.96, T.116, Y.117, Y.121, A.122, G.124, Y.125, F.126, K.128 19 PLIP interactions: 19 interactions with chain G Hydrophobic interactions: G:Q.34, G:L.35, G:Y.125, G:F.126 Hydrogen bonds: G:C.83, G:V.85, G:Q.90, G:V.91, G:K.92, G:G.93, G:Y.94, G:G.95, G:T.96, G:T.96, G:T.116, G:Y.117, G:Y.121 Water bridges: G:Y.125 Salt bridges: G:K.128 MLC.8: 22 residues within 4Å: Chain H: Q.34, L.35, M.38, V.81, C.83, A.84, V.85, Q.90, V.91, K.92, G.93, Y.94, G.95, T.96, T.116, Y.117, Y.121, A.122, G.124, Y.125, F.126, K.128 19 PLIP interactions: 19 interactions with chain H Hydrophobic interactions: H:Q.34, H:L.35, H:Y.125 Hydrogen bonds: H:C.83, H:C.83, H:V.85, H:Q.90, H:V.91, H:K.92, H:G.93, H:Y.94, H:G.95, H:T.96, H:T.116, H:Y.117, H:Y.121, H:K.128 Water bridges: H:D.119 Salt bridges: H:K.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, S. et al., Molecular Basis of KAT2A Selecting Acyl-CoA Cofactors for Histone Modifications. Res (2023)

Release Date

2023-05-03

Peptides

Histone acetyltransferase KAT2A: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

D
F

E
B

F
A

G
G

H
H

Histone acetyltransferase KAT2A

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