SMTL ID : 4xrp.1

Structure of the Pnkp1/Rnl/Hen1 RNA repair complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

hetero-2-2-2-mer

Ligands

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

PO4.1: 9 residues within 4Å: Chain A: A.19, P.20, G.21, S.22, G.23, K.24, S.25, D.85, R.126 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:A.19, A:G.21, A:S.22, A:G.23, A:K.24, A:S.25 Salt bridges: A:K.24, A:R.126 PO4.13: 8 residues within 4Å: Chain D: A.19, P.20, G.21, S.22, G.23, K.24, S.25, T.26 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:A.19, D:G.21, D:S.22, D:G.23, D:K.24, D:S.25, D:S.25, D:T.26 Salt bridges: D:K.24

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.183, D.185, D.288, R.289 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.183, A:D.185, A:D.288 MG.5: 2 residues within 4Å: Chain B: E.43 Ligands: SO4.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.43 MG.6: 3 residues within 4Å: Chain B: K.60, K.61, E.120 No protein-ligand interaction detected (PLIP) MG.14: 5 residues within 4Å: Chain D: D.183, D.185, K.268, D.287, D.288 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.183, D:D.185, D:D.288

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

SO4.3: 4 residues within 4Å: Chain A: Y.169, A.170, Q.172, F.281 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.172, A:Q.172 SO4.4: 2 residues within 4Å: Chain A: D.249, Y.250 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.250, A:Y.250 SO4.7: 5 residues within 4Å: Chain B: S.32, V.33, E.34, E.43 Ligands: MG.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.33, B:E.34, B:E.43 SO4.9: 4 residues within 4Å: Chain C: L.31, H.78, E.82, K.194 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:H.78, C:K.194 SO4.15: 5 residues within 4Å: Chain E: I.26, Q.118, F.234, K.299, P.310 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Q.118, E:Q.118 Salt bridges: E:K.299 SO4.16: 5 residues within 4Å: Chain E: K.31, S.32, V.33, E.34, E.43 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:V.33, E:E.34, E:E.43 SO4.17: 4 residues within 4Å: Chain F: N.17, N.19, K.100, W.101 No protein-ligand interaction detected (PLIP) SO4.18: 4 residues within 4Å: Chain F: H.78, E.82, K.194, Y.195 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:E.82, F:Y.195 Salt bridges: F:H.78, F:K.194

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 6 residues within 4Å: Chain B: S.23, P.24, I.26, Y.66, R.83, E.120 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.23, B:E.120 GOL.10: 7 residues within 4Å: Chain C: S.125, T.126, W.127, T.178, L.212, R.216, F.377 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.126, C:T.126, C:T.178, C:R.216, C:R.216 GOL.11: 6 residues within 4Å: Chain C: S.125, Y.128, S.129, K.130, G.149, N.150 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.125, C:K.130, C:K.130, C:G.149, C:N.150 GOL.12: 7 residues within 4Å: Chain C: V.205, P.206, Y.207, F.235, E.238, L.240, Y.375 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.207, C:E.238 GOL.19: 6 residues within 4Å: Chain F: S.125, T.126, W.127, T.178, L.212, R.216 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:S.125, F:T.126, F:W.127, F:R.216, F:R.216

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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