SMTL ID : 6qzw.2 (1 other biounit)

DPP8 bound to a dipeptide (MP) from the N-terminus of BRCA2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-dimer

Ligands

2 x MET- PRO: MET-PRO(Non-covalent)

MET-PRO.1: 13 residues within 4Å: Chain A: R.160, E.275, E.276, Y.669, Q.673, V.674, S.755, Y.756, Y.787, Y.791, N.835, V.836, H.865 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.791, A:Y.791, A:V.836 Hydrogen bonds: A:R.160, A:E.276, A:Y.669, A:S.755, A:Y.756, A:Y.787, A:N.835 Salt bridges: A:H.865 MET-PRO.3: 13 residues within 4Å: Chain B: R.160, E.275, E.276, Y.669, Q.673, V.674, S.755, Y.756, Y.787, Y.791, N.835, V.836, H.865 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.791, B:Y.791, B:V.836 Hydrogen bonds: B:R.160, B:E.275, B:S.755, B:Y.756, B:Y.787, B:N.835 Salt bridges: B:H.865

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 5 residues within 4Å: Chain A: R.158, Q.274, E.275, D.278, Y.280 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.275, A:D.278, A:Y.280 NA.4: 5 residues within 4Å: Chain B: R.158, Q.274, E.275, D.278, Y.280 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.274

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Silva-Garcia, M. et al., Dipeptidyl peptidase 9 triggers BRCA2 degradation by the N-degron pathway to promote DNA-damage repair. Biorxiv (2020)

Release Date

2020-09-30

Peptides

Dipeptidyl peptidase 8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
C

Dipeptidyl peptidase 8

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