SMTL ID : 5hjd.1 (1 other biounit)

AF9 YEATS in complex with histone H3 Crotonylation at K18

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

homo-tetramer

Ligands

4 x LYS- ALA- PRO- ARG- KCR- GLN- LEU: peptide of Histone H3.1(Non-covalent)

LYS-ALA-PRO-ARG-KCR-GLN-LEU.1: 12 residues within 4Å: Chain D: F.30, H.58, S.60, F.61, G.79, Y.80, A.81, G.82, F.83, D.105, L.108, L.110 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:F.30, D:F.61, D:F.61, D:F.61, D:Y.80, D:F.83, D:F.83 Hydrogen bonds: D:S.60, D:S.60, D:Y.80, D:G.82, D:G.82, D:L.106 Salt bridges: D:D.105 LYS-ALA-PRO-ARG-KCR-GLN-LEU.2: 15 residues within 4Å: Chain A: F.30, H.58, E.59, S.60, F.61, G.79, Y.80, A.81, G.82, F.83, D.105, L.106, F.107, L.108, L.110 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.30, A:H.58, A:F.61, A:F.61, A:Y.80, A:A.81 Hydrogen bonds: A:E.59, A:S.60, A:S.60, A:Y.80, A:G.82, A:G.82, A:F.83 Salt bridges: A:D.105 LYS-ALA-PRO-ARG-KCR-GLN-LEU.3: 13 residues within 4Å: Chain B: F.30, H.58, S.60, F.61, G.79, Y.80, A.81, G.82, F.83, I.84, D.105, L.106, F.107 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.30, B:F.61, B:F.61, B:Y.80, B:A.81 Hydrogen bonds: B:S.60, B:S.60, B:Y.80, B:A.81, B:G.82, B:G.82, B:F.83, B:L.106 Salt bridges: B:D.105 LYS-ALA-PRO-ARG-KCR-GLN-LEU.4: 14 residues within 4Å: Chain C: F.30, H.58, S.60, F.61, G.79, Y.80, A.81, G.82, F.83, I.84, D.105, F.107, L.108, L.110 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:F.30, C:F.30, C:H.58, C:F.61, C:F.61, C:F.61, C:A.81 Hydrogen bonds: C:S.60, C:S.60, C:Y.80, C:A.81, C:G.82, C:G.82, C:F.83 Salt bridges: C:D.105

3 x CU: COPPER (II) ION(Non-covalent)

CU.5: 2 residues within 4Å: Chain A: F.107, H.109 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.109 CU.7: 1 residues within 4Å: Chain B: H.43 No protein-ligand interaction detected (PLIP) CU.8: 1 residues within 4Å: Chain B: H.118 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.118

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 4 residues within 4Å: Chain A: R.101, F.102, D.103, R.120 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.103 Salt bridges: A:R.120 SO4.9: 2 residues within 4Å: Chain B: R.39, H.43 No protein-ligand interaction detected (PLIP) SO4.10: 3 residues within 4Å: Chain C: F.102, D.103, R.120 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.103 Salt bridges: C:R.120 SO4.11: 5 residues within 4Å: Chain D: R.18, M.35, F.37, R.39, K.74 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.18 Salt bridges: D:R.39, D:K.74 SO4.12: 2 residues within 4Å: Chain D: Y.90, K.99 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.90 Salt bridges: D:K.99 SO4.13: 4 residues within 4Å: Chain C: A.4 Chain D: K.12, P.41, E.42 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:K.12 SO4.14: 3 residues within 4Å: Chain A: R.18, R.39 Chain D: H.118 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:R.18 Salt bridges: A:R.39, D:H.118 SO4.15: 3 residues within 4Å: Chain D: R.22, T.26, V.27 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.22, D:V.27

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Y.Y. et al., Molecular Coupling of Histone Crotonylation and Active Transcription by AF9 YEATS Domain. Mol.Cell (2016)

Release Date

2016-04-20

Peptides

Protein AF-9: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
G

Protein AF-9

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