SMTL ID : 8gxc.1

Crystal structure of NAD+ -II riboswitch in complex with NMN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-pentamer

Ligands

2 x NMN: BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE(Non-functional Binders)

NMN.1: 10 residues within 4Å: Chain A: C.5, G.6, U.7, C.40, G.41, G.42, A.53, C.54, A.55 Ligands: MG.2 No protein-ligand interaction detected (PLIP) NMN.8: 9 residues within 4Å: Chain B: C.5, G.6, U.7, C.40, G.41, G.42, A.53, C.54, A.55 No protein-ligand interaction detected (PLIP)

16 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2: 2 residues within 4Å: Chain A: G.42 Ligands: NMN.1 No protein-ligand interaction detected (PLIP) MG.3: 2 residues within 4Å: Chain A: U.8, C.13 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain A: A.9, C.10, G.11 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain A: A.18, G.59 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain A: A.61 Chain B: C.10 No protein-ligand interaction detected (PLIP) MG.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain A: U.12 Chain B: C.10 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain B: G.6, U.7, C.14, G.15 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain B: C.10, G.11 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain B: G.36 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain B: A.53, C.54 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Chain B: A.61 No protein-ligand interaction detected (PLIP) MG.15: 1 residues within 4Å: Chain B: G.1 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain B: G.41, A.55 No protein-ligand interaction detected (PLIP) MG.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, X. et al., Structure-based investigations of the NAD+-II riboswitch. Nucleic Acids Res. (2023)

Release Date

2023-01-18

Peptides

U1 small nuclear ribonucleoprotein A: CDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
C

D
D

E
E

F
F

G
G

U1 small nuclear ribonucleoprotein A

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