SMTL ID : 9b2d.1

Yeast Rad51-ssDNA filament

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 20 residues within 4Å: Chain A: R.188, T.189, G.190, K.191, S.192, Q.193, R.228, R.368, I.387, E.389 Chain B: V.373, D.374, S.375, P.376, C.377, L.378, P.379, E.380 Ligands: AF3.2, MG.3 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.188, A:T.189, A:G.190, A:K.191, A:S.192, A:Q.193, A:Q.193, A:R.368, B:C.377, B:E.380 Salt bridges: A:K.191 ADP.4: 20 residues within 4Å: Chain B: R.188, T.189, G.190, K.191, S.192, Q.193, R.228, R.368, I.387, E.389 Chain C: V.373, D.374, S.375, P.376, C.377, L.378, P.379, E.380 Ligands: AF3.5, MG.6 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:R.188, B:T.189, B:G.190, B:K.191, B:S.192, B:Q.193, B:Q.193, B:R.368, C:C.377, C:E.380, C:E.380, C:E.380 Salt bridges: B:K.191 ADP.7: 20 residues within 4Å: Chain C: R.188, T.189, G.190, K.191, S.192, Q.193, R.228, R.368, I.387, E.389 Chain D: V.373, D.374, S.375, P.376, C.377, L.378, P.379, E.380 Ligands: AF3.8, MG.9 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.188, C:T.189, C:T.189, C:G.190, C:K.191, C:S.192, C:S.192, C:Q.193, C:Q.193, C:R.368, D:C.377 Salt bridges: C:K.191 ADP.10: 12 residues within 4Å: Chain D: R.188, T.189, G.190, K.191, S.192, Q.193, R.228, R.368, I.387, E.389 Ligands: AF3.11, MG.12 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:R.188, D:T.189, D:T.189, D:G.190, D:K.191, D:S.192, D:Q.193, D:Q.193, D:R.368, D:E.389 Salt bridges: D:K.191 ADP.13: 20 residues within 4Å: Chain E: R.188, T.189, G.190, K.191, S.192, Q.193, R.228, R.368, I.387, E.389 Chain F: V.373, D.374, S.375, P.376, C.377, L.378, P.379, E.380 Ligands: AF3.14, MG.15 10 PLIP interactions: 9 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:R.188, E:T.189, E:G.190, E:K.191, E:S.192, E:Q.193, E:Q.193, E:R.368, F:C.377 Salt bridges: E:K.191 ADP.16: 19 residues within 4Å: Chain A: D.374, S.375, P.376, C.377, L.378, P.379, E.380 Chain F: R.188, T.189, G.190, K.191, S.192, Q.193, R.228, R.368, I.387, E.389 Ligands: AF3.17, MG.18 11 PLIP interactions: 1 interactions with chain A, 10 interactions with chain F Hydrogen bonds: A:E.380, F:R.188, F:T.189, F:G.190, F:K.191, F:S.192, F:Q.193, F:Q.193, F:R.368, F:E.389 Salt bridges: F:K.191

6 x AF3: ALUMINUM FLUORIDE(Covalent)(Non-covalent)

AF3.2: 7 residues within 4Å: Chain A: K.191, S.192, E.221, T.223, D.280 Ligands: ADP.1, MG.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.192 AF3.5: 7 residues within 4Å: Chain B: K.191, S.192, E.221, T.223, D.280 Ligands: ADP.4, MG.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.192 AF3.8: 7 residues within 4Å: Chain C: K.191, S.192, E.221, T.223, D.280 Ligands: ADP.7, MG.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.192 AF3.11: 6 residues within 4Å: Chain D: S.192, E.221, T.223, D.280 Ligands: ADP.10, MG.12 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.192 AF3.14: 6 residues within 4Å: Chain E: S.192, E.221, T.223, D.280 Ligands: ADP.13, MG.15 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.192 AF3.17: 7 residues within 4Å: Chain F: K.191, S.192, E.221, T.223, D.280 Ligands: ADP.16, MG.18 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.192

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 3 residues within 4Å: Chain B: H.352 Ligands: ADP.1, AF3.2 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Ligands: ADP.4, AF3.5 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain D: H.352 Ligands: ADP.7, AF3.8 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Ligands: ADP.10, AF3.11 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain F: H.352 Ligands: ADP.13, AF3.14 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain A: H.352 Ligands: ADP.16, AF3.17 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, J. et al., Yeast Rad51-ssDNA filament. To Be Published

Release Date

2025-01-29

Peptides

DNA repair protein RAD51: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

D
F

E
A

F
B

DNA repair protein RAD51

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