SMTL ID : 6sus.1

Crystal structure of RTX domain blocks IV and V of adenylate cyclase toxin from Bordetella pertussis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

monomer

Ligands

15 x CA: CALCIUM ION(Non-covalent)

CA.1: 7 residues within 4Å: Chain A: D.43, Q.45, N.47, G.60, G.61, E.62, D.65 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.43, A:Q.45, A:G.60, A:E.62, A:D.65 CA.2: 7 residues within 4Å: Chain A: G.61, E.62, G.63, D.65, G.78, A.80, D.83 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:G.61, A:G.63, A:G.78, A:A.80, A:D.83 CA.3: 6 residues within 4Å: Chain A: D.79, A.80, G.81, D.83, N.100, N.103 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.79, A:G.81, A:D.83, H2O.2 CA.4: 7 residues within 4Å: Chain A: S.160, R.162, D.164, G.177, L.178, A.179, D.182 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:S.160, A:R.162, A:D.164, A:G.177, A:D.182 CA.5: 7 residues within 4Å: Chain A: L.178, A.179, G.180, D.182, G.195, E.197, D.200 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:G.180, A:D.182, A:G.195, A:E.197, A:D.200 CA.6: 8 residues within 4Å: Chain A: D.196, E.197, G.198, D.200, G.213, G.214, Q.215, D.218 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.196, A:G.198, A:D.200, A:G.213, A:D.218 CA.7: 7 residues within 4Å: Chain A: G.214, Q.215, G.216, D.218, E.233, G.235, D.239 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:G.214, A:G.216, A:D.218, A:E.233, A:D.239 CA.8: 4 residues within 4Å: Chain A: G.236, D.239, R.282, E.284 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.236, A:D.239, A:R.282, A:E.284, H2O.2 CA.9: 6 residues within 4Å: Chain A: D.205, A.206, G.207, D.209, Y.226, D.229 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.205, A:G.207, A:D.209, A:Y.226, A:D.229 CA.10: 7 residues within 4Å: Chain A: G.187, A.188, G.189, D.191, G.204, A.206, D.209 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:G.187, A:G.189, A:D.191, A:G.204, A:D.209 CA.11: 7 residues within 4Å: Chain A: D.169, G.171, N.173, G.186, G.187, A.188, D.191 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.169, A:G.171, A:G.186, A:A.188, A:D.191 CA.12: 7 residues within 4Å: Chain A: A.52, G.54, D.56, G.69, G.70, D.71, D.74 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:A.52, A:G.54, A:D.56, A:G.69, A:D.74 CA.13: 8 residues within 4Å: Chain A: G.70, D.71, G.72, D.74, G.87, E.88, A.89, D.92 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:G.70, A:G.72, A:D.74, A:G.87, A:D.92 CA.14: 8 residues within 4Å: Chain A: E.88, A.89, G.90, D.92, G.107, G.108, D.109, D.112 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.88, A:G.90, A:D.92, A:G.107, A:D.112 CA.15: 6 residues within 4Å: Chain A: G.108, D.109, G.110, D.112, N.153, E.155 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:G.108, A:G.110, A:D.112, A:N.153, A:E.155

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.16: 6 residues within 4Å: Chain A: R.82, D.83, R.84, G.102, L.104, V.150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.82, A:R.82 PGE.21: 4 residues within 4Å: Chain A: A.206, V.224, G.225, Y.226 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.17: 6 residues within 4Å: Chain A: W.93, T.113, N.156, V.158, V.174, N.176 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.113, A:N.156, A:N.176 GOL.18: 2 residues within 4Å: Chain A: N.176, L.178 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.176 Water bridges: A:D.196

1 x NO3: NITRATE ION(Non-functional Binders)

NO3.19: 4 residues within 4Å: Chain A: F.212, G.214, Y.232, S.234 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.214 Water bridges: A:S.234, A:S.234

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.20: 6 residues within 4Å: Chain A: N.208, D.209, D.210, H.228, D.229, T.230 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.209, A:T.230, A:T.230 EDO.22: 4 residues within 4Å: Chain A: F.95, Q.96, D.97, G.118 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.95 Water bridges: A:Q.96, A:A.98 EDO.23: 6 residues within 4Å: Chain A: I.167, G.168, D.169, A.170, G.187, A.188 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.188 Water bridges: A:S.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Motlova, L. et al., Continuous Assembly of beta-Roll Structures Is Implicated in the Type I-Dependent Secretion of Large Repeat-in-Toxins (RTX) Proteins. J.Mol.Biol. (2020)

Release Date

2020-09-16

Peptides

Bifunctional hemolysin/adenylate cyclase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bifunctional hemolysin/adenylate cyclase