SMTL ID : 8jwj.2 (1 other biounit)

PHD Finger Protein 7 (PHF7) in complex with UBE2D2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.96 Å

Oligo State

hetero-1-1-mer

Ligands

7 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.11, C.14, H.36, C.39 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.11, A:C.14, A:H.36, A:C.39 ZN.2: 4 residues within 4Å: Chain A: C.76, C.79, H.98, C.101 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.76, A:C.79, A:H.98, A:C.101 ZN.3: 4 residues within 4Å: Chain A: C.88, C.93, C.119, H.122 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.88, A:C.93, A:C.119, A:H.122 ZN.4: 4 residues within 4Å: Chain A: C.138, C.141, H.164, C.167 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.138, A:C.141, A:H.164, A:C.167 ZN.5: 4 residues within 4Å: Chain A: C.157, C.158, C.182, C.185 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.157, A:C.158, A:C.182, A:C.185 ZN.6: 4 residues within 4Å: Chain A: C.226, C.231, H.260, C.263 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.226, A:C.231, A:H.260, A:C.263 ZN.7: 4 residues within 4Å: Chain A: C.251, C.254, C.275, C.278 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.251, A:C.254, A:C.275, A:C.278

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 9 residues within 4Å: Chain A: P.21, E.22, E.26, Y.37, F.38, H.173, H.201, R.205 Ligands: MPD.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.26, A:R.205, A:R.205 GOL.12: 3 residues within 4Å: Chain B: L.15, R.27, A.28 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.18, B:A.28 GOL.13: 8 residues within 4Å: Chain A: F.216, E.218, L.219 Chain B: K.71, V.72, S.88, I.89, L.94 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.218, B:V.72, B:V.72, B:I.89 GOL.14: 4 residues within 4Å: Chain B: F.56, T.75, T.76, Y.150 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.75, B:T.75, B:Y.150

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.9: 6 residues within 4Å: Chain A: E.26, L.28, H.57, P.203, R.205 Ligands: GOL.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.28, A:P.203 Hydrogen bonds: A:R.205 MPD.10: 7 residues within 4Å: Chain A: I.41, S.43, L.46, Q.48, F.59, E.114, Y.115 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.41, A:S.43

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

SO4.11: 4 residues within 4Å: Chain A: Y.37, Q.48, H.57, Y.115 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.37, A:Q.48, A:Q.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, H.S. et al., Molecular basis for PHF7-mediated ubiquitination of histone H3. Genes Dev. (2023)

Release Date

2023-12-20

Peptides

PHD finger protein 7: A
Ubiquitin-conjugating enzyme E2 D2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

PHD finger protein 7

Ubiquitin-conjugating enzyme E2 D2

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