SMTL ID : 4xru.1

Structure of Pnkp1/Rnl/Hen1 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.41 Å

Oligo State

hetero-oligomer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.183, D.185, D.288 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.183, A:D.185, A:D.288, A:D.288 MG.7: 4 residues within 4Å: Chain B: Y.62, G.64, E.120 Ligands: ATP.3 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain C: Q.64, Q.68, Y.122, Y.181 No protein-ligand interaction detected (PLIP) MG.12: 4 residues within 4Å: Chain D: D.183, D.185, D.287, D.288 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.183, D:D.185, D:D.288, H2O.3 MG.15: 5 residues within 4Å: Chain E: Y.62, M.63, E.120, E.294 Ligands: ATP.14 No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain F: Q.64, Q.68, Y.122, Y.181 No protein-ligand interaction detected (PLIP)

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 12 residues within 4Å: Chain A: A.19, P.20, G.21, S.22, G.23, K.24, S.25, T.26, T.87, R.122 Chain B: N.370, E.372 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.21, A:S.22, A:G.23, A:K.24, A:S.25, A:S.25, A:T.26, A:T.26, A:R.122 Salt bridges: A:K.24, A:K.24 pi-Cation interactions: A:R.122, A:R.122 ATP.3: 17 residues within 4Å: Chain B: T.25, I.26, E.59, K.60, K.61, Y.62, Y.66, R.83, E.120, F.234, E.294, K.299, K.313, R.315, K.344, L.394 Ligands: MG.7 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:I.26, B:I.26, B:E.59, B:K.61, B:Y.62, B:K.299, B:R.315 Water bridges: B:R.83, B:L.394 Salt bridges: B:K.61, B:R.83, B:K.313, B:K.313, B:K.313, B:K.344 pi-Stacking: B:F.234 ATP.13: 8 residues within 4Å: Chain D: P.20, G.21, G.23, K.24, S.25, T.26 Chain E: N.370, E.372 14 PLIP interactions: 10 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:G.21, D:G.23, D:K.24, D:S.25, D:S.25, D:S.25, D:T.26, D:T.26, D:D.85, E:N.370, E:N.370, E:Y.371, E:E.372 Salt bridges: D:K.24 ATP.14: 16 residues within 4Å: Chain E: T.25, I.26, E.59, K.60, K.61, Y.62, Y.66, R.83, E.120, F.234, E.294, K.299, K.313, R.315, L.394 Ligands: MG.15 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:I.26, E:E.59, E:K.61, E:Y.62, E:R.83, E:R.315, E:L.394 Salt bridges: E:K.61, E:K.313, E:K.313, E:K.313 pi-Stacking: E:F.234

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.4: 6 residues within 4Å: Chain B: S.32, V.33, E.34, Y.42, E.43, L.46 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.33, B:E.34, B:E.34 Salt bridges: B:E.43

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain B: E.37, I.38, E.39, R.282, N.289, R.315, N.316, N.317 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.38, B:E.39, B:E.39, B:R.282, B:N.317 GOL.6: 8 residues within 4Å: Chain B: T.78, I.88, N.89, H.90, L.91, Q.93, C.96, L.97 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.78, B:H.90, B:L.91, B:Q.93

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 4 residues within 4Å: Chain B: N.250, D.251, R.301, T.302 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.251, B:R.301 Salt bridges: B:R.301 PO4.11: 7 residues within 4Å: Chain C: N.369, C.416, G.417, G.424, E.425, T.426, Q.429 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.369, C:E.425, C:T.426 PO4.16: 4 residues within 4Å: Chain E: D.110, V.112, Y.241, R.245 2 PLIP interactions: 2 interactions with chain E Water bridges: E:E.239 Salt bridges: E:R.245 PO4.19: 8 residues within 4Å: Chain F: Y.57, P.59, Q.68, S.72, L.74, H.176, Y.181, Y.184 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:S.72, F:Y.184 Salt bridges: F:H.176 PO4.20: 7 residues within 4Å: Chain F: N.369, P.395, G.417, G.424, E.425, T.426, Q.429 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:T.426, F:T.426, F:Q.429

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.9: 12 residues within 4Å: Chain C: R.253, I.270, G.271, D.296, T.297, D.298, T.337, E.338, V.339, H.342, T.344, L.351 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.271, C:T.297, C:D.298, C:T.337, C:E.338, C:T.344 Water bridges: C:G.271 Salt bridges: C:H.250, C:R.253, C:K.276 SAH.17: 12 residues within 4Å: Chain F: H.250, G.271, G.273, L.275, K.276, D.296, T.297, T.337, V.339, N.343, T.344, L.351 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:T.297, F:D.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, P. et al., Reconstitution and structure of a bacterial Pnkp1-Rnl-Hen1 RNA repair complex. Nat Commun (2015)

Release Date

2015-04-22

Peptides

Pnkp1: AD
Rnl: BE
Hen1: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

Pnkp1

Rnl

Hen1

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