SMTL ID : 6wat.1 (14 other biounits)

complex structure of PHF1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x AYA- THR- LYS- VAL- ALA- ARG- M3L- SER: Histone H3.1t peptide(Non-covalent)

AYA-THR-LYS-VAL-ALA-ARG-M3L-SER.1: 27 residues within 4Å: Chain A: R.14, W.15, G.18, L.19, L.20, Y.21, F.39, D.41, S.43, F.45, G.59, E.60, E.61 Chain B: D.10, V.11, L.12, L.22, T.24, Q.38, E.40, P.54, A.55, A.56, L.57 Ligands: UNX.8, UNX.10, UNX.13 26 PLIP interactions: 18 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:L.19, A:L.19, A:L.20, A:Y.21, B:L.12, B:L.22, B:L.22 Hydrogen bonds: A:R.14, A:R.14, A:L.20, A:L.20, A:E.61, B:D.10, B:T.24, B:P.54, B:A.56, B:A.56 Water bridges: A:Y.21, A:L.22, A:E.61, A:E.61 Salt bridges: A:D.41 pi-Cation interactions: A:W.15, A:W.15, A:Y.21, A:F.39 AYA-THR-LYS-VAL-ALA-ARG-M3L-SER.2: 24 residues within 4Å: Chain A: D.10, V.11, L.12, L.22, T.24, Q.38, E.40, P.54, A.55, A.56, L.57 Chain B: R.14, W.15, G.18, L.19, L.20, Y.21, F.39, D.41, S.43, F.45, E.60, E.61 Ligands: UNX.14 27 PLIP interactions: 16 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:L.19, B:L.19, B:L.20, B:Y.21, B:Y.21, A:L.12, A:L.22, A:L.22, A:A.55 Hydrogen bonds: B:R.14, B:R.14, B:L.20, B:L.20, B:E.60, A:D.10, A:T.24, A:T.24, A:P.54, A:A.56, A:A.56 Water bridges: B:L.22, A:F.39 Salt bridges: B:D.41 pi-Cation interactions: B:W.15, B:W.15, B:Y.21, B:F.39

12 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.3: 2 residues within 4Å: Chain A: F.45, L.46 No protein-ligand interaction detected (PLIP) UNX.4: 3 residues within 4Å: Chain A: L.48, K.50, D.51 No protein-ligand interaction detected (PLIP) UNX.5: 2 residues within 4Å: Chain A: S.43, Q.44 No protein-ligand interaction detected (PLIP) UNX.6: 3 residues within 4Å: Chain A: R.2, P.3, W.6 No protein-ligand interaction detected (PLIP) UNX.7: 1 residues within 4Å: Chain A: D.17 No protein-ligand interaction detected (PLIP) UNX.8: 4 residues within 4Å: Chain A: E.61 Chain B: A.55 Ligands: AYA-THR-LYS-VAL-ALA-ARG-M3L-SER.1, UNX.10 No protein-ligand interaction detected (PLIP) UNX.9: 2 residues within 4Å: Chain A: E.33, W.49 No protein-ligand interaction detected (PLIP) UNX.10: 5 residues within 4Å: Chain B: W.6, Q.9, P.54 Ligands: AYA-THR-LYS-VAL-ALA-ARG-M3L-SER.1, UNX.8 No protein-ligand interaction detected (PLIP) UNX.11: 3 residues within 4Å: Chain B: G.8, I.25, K.26 No protein-ligand interaction detected (PLIP) UNX.12: 2 residues within 4Å: Chain B: W.6, E.7 No protein-ligand interaction detected (PLIP) UNX.13: 2 residues within 4Å: Ligands: AYA-THR-LYS-VAL-ALA-ARG-M3L-SER.1, AYA-THR-LYS-VAL-ALA-ARG-M3L-SER.1 No protein-ligand interaction detected (PLIP) UNX.14: 3 residues within 4Å: Chain B: E.40 Ligands: AYA-THR-LYS-VAL-ALA-ARG-M3L-SER.2, AYA-THR-LYS-VAL-ALA-ARG-M3L-SER.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, C. et al., Structural basis for histone variant H3tK27me3 recognition by PHF1 and PHF19. Elife (2020)

Release Date

2020-08-26

Peptides

PHD finger protein 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AA

B
AC

PHD finger protein 1

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