SMTL ID : 5jre.1

Crystal structure of NeC3PO in complex with ssDNA.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-octamer

Ligands

5 x ADE: ADENINE(Non-covalent)

ADE.1: 5 residues within 4Å: Chain A: S.108, F.111, W.143, F.147 Chain B: M.105 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.143 Water bridges: A:D.195 pi-Stacking: A:F.111, A:F.111 ADE.2: 5 residues within 4Å: Chain A: M.105 Chain B: S.108, F.111, W.143, F.147 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.108, B:W.143 Water bridges: B:N.193 pi-Stacking: B:F.111, B:F.111 ADE.4: 7 residues within 4Å: Chain D: G.154, L.157, R.158, S.161, K.209 Chain G: D.201, N.205 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain G Hydrogen bonds: D:S.161, D:K.209, G:S.204, G:S.204, G:N.205 ADE.7: 6 residues within 4Å: Chain G: Y.107, S.108, F.111, W.143, F.147 Chain H: M.105 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain H pi-Stacking: G:F.111, G:F.111 Hydrogen bonds: H:M.105 ADE.8: 7 residues within 4Å: Chain C: D.201, N.205 Chain H: G.154, L.157, R.158, S.161, K.209 6 PLIP interactions: 3 interactions with chain H, 3 interactions with chain C Hydrogen bonds: H:S.161, H:K.209, H:K.209, C:N.205, C:N.205 Water bridges: C:S.204

3 x ADZ: 9-METHYL-9H-PURIN-6-AMINE(Non-covalent)

ADZ.3: 5 residues within 4Å: Chain C: S.108, F.111, W.143, F.147 Chain D: M.105 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:W.143 pi-Stacking: C:F.111, C:F.111 ADZ.5: 6 residues within 4Å: Chain E: M.105 Chain F: S.108, F.111, I.112, W.143, F.147 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:W.143 pi-Stacking: F:F.111, F:F.111 ADZ.6: 6 residues within 4Å: Chain E: Y.107, S.108, F.111, W.143, F.147 Chain F: M.105 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:W.143 Water bridges: E:N.193 pi-Stacking: E:F.111, E:F.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, J. et al., Structural basis for single-stranded RNA recognition and cleavage by C3PO. Nucleic Acids Res. (2016)

Release Date

2016-09-28

Peptides

NEQ131: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

NEQ131

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