SMTL ID : 8gxb.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-pentamer

Ligands

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-functional Binders)

NAD.1: 13 residues within 4Å: Chain A: A.3, G.4, C.5, G.6, U.7, A.16, C.40, G.41, G.42, A.53, C.54 Ligands: MG.6, MG.7 No protein-ligand interaction detected (PLIP) NAD.12: 12 residues within 4Å: Chain B: C.5, G.6, U.7, A.16, A.17, A.39, C.40, G.41, G.42, A.53, C.54, A.55 No protein-ligand interaction detected (PLIP)

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

MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.3: 1 residues within 4Å: Chain A: A.17 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain A: C.10, G.11 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain A: A.61 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Ligands: NAD.1 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain A: G.42 Ligands: NAD.1 No protein-ligand interaction detected (PLIP) MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Chain A: G.1 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Chain A: G.59 No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Chain A: C.38 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain A: G.11, U.12 Chain B: C.10 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Chain B: G.1 No protein-ligand interaction detected (PLIP) MG.15: 4 residues within 4Å: Chain B: G.6, U.7, C.14, G.15 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain B: C.10, G.11 No protein-ligand interaction detected (PLIP) MG.17: 1 residues within 4Å: Chain B: A.61 No protein-ligand interaction detected (PLIP) MG.18: 1 residues within 4Å: Chain B: G.59 No protein-ligand interaction detected (PLIP) MG.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.20: 1 residues within 4Å: Chain B: C.32 No protein-ligand interaction detected (PLIP) MG.21: 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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