SMTL ID : 7rah.1

Adenylate cyclase toxin RTX domain fragment bound to M1H5 Fab and M2B10 Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-1-1-1-mer

Ligands

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 3 residues within 4Å: Chain A: E.186, R.189, H.190 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.156 Salt bridges: A:R.189, A:H.190

19 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain E: G.51, G.53, D.55, G.70, A.72, D.75 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:G.51, E:G.53, E:G.70, E:A.72, E:D.75 CA.3: 6 residues within 4Å: Chain E: G.71, A.72, G.73, D.75, N.122, E.124 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:G.71, E:G.73, E:D.75, E:E.124, H2O.7 CA.4: 6 residues within 4Å: Chain E: S.129, L.131, D.133, G.146, D.148, D.151 6 PLIP interactions: 6 interactions with chain E Metal complexes: E:S.129, E:L.131, E:D.133, E:G.146, E:D.148, E:D.151 CA.5: 6 residues within 4Å: Chain E: D.138, Q.140, N.142, G.155, G.157, D.160 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.138, E:Q.140, E:G.155, E:G.157, E:D.160 CA.6: 8 residues within 4Å: Chain E: H.147, D.148, G.149, D.151, G.164, G.165, L.166, D.169 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:G.149, E:G.164, E:L.166, E:D.169, E:D.169 CA.7: 8 residues within 4Å: Chain E: R.156, G.157, G.158, D.160, G.173, E.174, D.175, D.178 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:R.156, E:G.158, E:D.160, E:G.173, E:D.178 CA.8: 5 residues within 4Å: Chain E: G.165, G.167, D.169, E.185, D.189 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:G.165, E:G.167, E:D.169, E:E.185, E:D.189 CA.9: 8 residues within 4Å: Chain E: E.174, D.175, G.176, D.178, G.193, G.194, A.195, D.198 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:E.174, E:G.176, E:D.178, E:G.193, E:D.198 CA.10: 6 residues within 4Å: Chain E: G.194, A.195, G.196, D.198, N.246, E.248 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:G.194, E:G.196, E:D.198, E:E.248, H2O.7 CA.11: 7 residues within 4Å: Chain E: T.253, M.255, D.257, G.270, Q.271, G.272, D.275 6 PLIP interactions: 6 interactions with chain E Metal complexes: E:T.253, E:M.255, E:D.257, E:G.270, E:G.272, E:D.275 CA.12: 7 residues within 4Å: Chain E: D.262, Q.264, N.266, G.279, G.280, D.281, D.284 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.262, E:Q.264, E:G.279, E:D.281, E:D.284 CA.13: 7 residues within 4Å: Chain E: Q.271, G.272, G.273, D.275, G.288, D.290, D.293 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:Q.271, E:G.273, E:D.275, E:G.288, E:D.293 CA.14: 7 residues within 4Å: Chain E: G.280, D.281, G.282, D.284, G.297, A.299, D.302 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:G.280, E:G.282, E:D.284, E:G.297, E:D.302 CA.15: 8 residues within 4Å: Chain E: G.289, D.290, G.291, D.293, G.306, G.307, L.308, D.311 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:G.289, E:G.291, E:D.293, E:G.306, E:D.311 CA.16: 7 residues within 4Å: Chain E: D.298, A.299, G.300, D.302, G.315, E.329, D.331 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.298, E:G.300, E:G.315, E:E.329, E:D.331 CA.17: 8 residues within 4Å: Chain E: G.307, L.308, G.309, D.311, G.335, G.336, D.337, D.340 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:G.307, E:G.309, E:G.335, E:D.337, E:D.340 CA.18: 5 residues within 4Å: Chain E: G.316, E.329, D.331, Y.348, D.351 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:G.316, E:D.331, E:Y.348, E:D.351, E:D.351 CA.19: 6 residues within 4Å: Chain E: G.336, D.337, G.338, D.340, E.355, D.361 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:G.336, E:G.338, E:D.340, E:E.355, E:D.361 CA.20: 6 residues within 4Å: Chain E: E.355, S.356, G.357, G.358, G.359, D.361 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.355, E:S.356, E:D.361

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goldsmith, J.A. et al., Structural basis for antibody binding to adenylate cyclase toxin reveals RTX linkers as neutralization-sensitive epitopes. Plos Pathog. (2021)

Release Date

2021-09-15

Peptides

M1H5 Fab Light Chain: A
M1H5 Fab Heavy Chain: B
M2B10 Fab Light Chain: C
M2B10 Fab Heavy Chain: D
Bifunctional adenylate cyclase toxin/hemolysin CyaA,Bifunctional adenylate cyclase toxin/hemolysin CyaA: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

M1H5 Fab Light Chain

M1H5 Fab Heavy Chain

M2B10 Fab Light Chain

M2B10 Fab Heavy Chain

Bifunctional adenylate cyclase toxin/hemolysin CyaA,Bifunctional adenylate cyclase toxin/hemolysin CyaA