SMTL ID : 5zb2.1

Crystal structure of Rad7 and Elc1 complex in yeast

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-2-2-mer

Ligands

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: I.255, T.259, A.260, Y.286 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.255 GOL.2: 4 residues within 4Å: Chain A: S.85, M.109, C.110, G.111 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.109, A:G.111 Water bridges: A:Q.112 GOL.3: 3 residues within 4Å: Chain A: L.76, K.77, R.78 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.77, A:R.78, A:R.78 Water bridges: A:N.51 GOL.4: 1 residues within 4Å: Chain A: R.302 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.302 GOL.5: 5 residues within 4Å: Chain A: H.209, S.210, R.239, K.240, E.269 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.210, A:R.239, A:R.239, A:E.269 GOL.11: 4 residues within 4Å: Chain C: I.255, T.259, A.260, Y.286 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:I.255 GOL.12: 4 residues within 4Å: Chain C: S.85, M.109, C.110, G.111 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:M.109, C:G.111 Water bridges: C:Q.112 GOL.13: 3 residues within 4Å: Chain C: L.76, K.77, R.78 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.77, C:R.78, C:R.78 Water bridges: C:N.51 GOL.14: 1 residues within 4Å: Chain C: R.302 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.302 GOL.15: 5 residues within 4Å: Chain C: H.209, S.210, R.239, K.240, E.269 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.210, C:R.239, C:R.239, C:E.269

2 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.6: 3 residues within 4Å: Chain A: Y.120, E.123, K.124 No protein-ligand interaction detected (PLIP) PG0.16: 3 residues within 4Å: Chain C: Y.120, E.123, K.124 No protein-ligand interaction detected (PLIP)

2 x P33: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL(Non-covalent)

P33.7: 16 residues within 4Å: Chain A: W.23, Q.24, D.28, F.35, Q.69 Chain C: W.23, Q.24, A.27, D.28, S.31, F.35, Q.69, F.98 Ligands: 9FO.9, P33.17, 9FO.19 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:D.28, A:D.28 P33.17: 16 residues within 4Å: Chain A: W.23, Q.24, A.27, D.28, S.31, F.35, Q.69, F.98 Chain C: W.23, Q.24, D.28, F.35, Q.69 Ligands: P33.7, 9FO.9, 9FO.19 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:D.28, A:D.28

2 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.8: 7 residues within 4Å: Chain A: F.89, N.114, E.116 Chain C: F.89, N.114, E.116 Ligands: P6G.18 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Water bridges: C:N.114, A:N.114 P6G.18: 7 residues within 4Å: Chain A: F.89, N.114, E.116 Chain C: F.89, N.114, E.116 Ligands: P6G.8 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Water bridges: C:N.114, A:N.114

2 x 9FO: 3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57-nonadecaoxanonapentacontane-1,59-diol(Non-covalent)

9FO.9: 25 residues within 4Å: Chain A: Q.24, D.65, H.66, Q.69, D.90, G.91, T.94, I.97, F.98, Y.120 Chain C: Q.24, D.65, H.66, Q.69, L.72, D.90, G.91, T.94, I.97, Y.120 Ligands: P33.7, NA.10, P33.17, 9FO.19, NA.20 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:Q.24, C:T.94, A:Q.24 Water bridges: A:T.94, A:T.94 9FO.19: 25 residues within 4Å: Chain A: Q.24, D.65, H.66, Q.69, L.72, D.90, G.91, T.94, I.97, Y.120 Chain C: Q.24, D.65, H.66, Q.69, D.90, G.91, T.94, I.97, F.98, Y.120 Ligands: P33.7, 9FO.9, NA.10, P33.17, NA.20 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:Q.24, A:Q.24, A:T.94 Water bridges: C:T.94, C:T.94

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

NA.10: 2 residues within 4Å: Ligands: 9FO.9, 9FO.19 2 PLIP interactions: 2 interactions with chain C Water bridges: C:T.94, C:T.94 NA.20: 2 residues within 4Å: Ligands: 9FO.9, 9FO.19 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, L. et al., Crystal structure of the yeast Rad7-Elc1 complex and assembly of the Rad7-Rad16-Elc1-Cul3 complex. DNA Repair (Amst.) (2019)

Release Date

2019-02-27

Peptides

DNA repair protein RAD7: AC
Elongin-C: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

DNA repair protein RAD7

Elongin-C