SMTL ID : 8ka0.2 (3 other biounits)

Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-bound calmodulin and a nicotinamide adenine dinucleotide (NAD+)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 19 residues within 4Å: Chain A: F.43, F.123, W.124, S.125, G.126, D.149, I.150, I.159, F.192, T.195, S.199, R.219, G.221, N.222, Y.223, F.224, Q.228, R.276, D.299 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:W.124, A:T.195, A:Y.223 Hydrogen bonds: A:W.124, A:W.124, A:W.124, A:G.126, A:D.149, A:S.199, A:G.221, A:N.222, A:N.222, A:Y.223, A:F.224, A:Q.228, A:R.276, A:R.276 Water bridges: A:D.149, A:R.219 Salt bridges: A:R.219 pi-Stacking: A:F.192 pi-Cation interactions: A:R.276

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: E.17, A.20, N.21, R.24 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.21, A:R.24, A:R.24 GOL.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain B: D.23, K.24, D.25, D.27, T.29 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.23, B:D.27, B:T.29 CA.4: 4 residues within 4Å: Chain B: D.96, D.98, N.100, Y.102 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.96, B:D.98, B:Y.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Choi, S. et al., Dissemination of pathogenic bacteria is reinforced by a MARTX toxin effector duet. Nat Commun (2024)

Release Date

2024-07-10

Peptides

RDTND-RID CBD: A
Calmodulin-2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

RDTND-RID CBD

Calmodulin-2

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