9MXI

Crystal Structure of synthetic antibody, COP-2, in complex with the C-terminal domain of Clostridium perfringens Enterotoxin

PDB DOI: https://doi.org/10.2210/pdb9MXI/pdb

Classification: IMMUNE SYSTEM/TOXIN
Organism(s): synthetic construct, Clostridium perfringens
Expression System: Escherichia coli BL21, Trichoplusia ni
Mutation(s): No

Deposited: 2025-01-20 Released: 2025-02-12
Deposition Author(s): Ogbu, C.P., Kapoor, S., Vecchio, A.J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.233 (Depositor), 0.236 (DCC)
R-Value Work:
0.182 (Depositor), 0.189 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of synthetic antibody, COP-2, in complex with the C-terminal domain of Clostridium perfringens Enterotoxin

Ogbu, C.P., Kapoor, S., Vecchio, A.J.

To be published.

Macromolecule Content

Total Structure Weight: 208.01 kDa
Atom Count: 13,393
Modelled Residue Count: 1,659
Deposited Residue Count: 1,899
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COP-2 antibody light chain	A [auth B], B [auth D], I [auth F]	239	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat-labile enterotoxin B chain	C [auth G], D [auth H], E [auth I]	134	Clostridium perfringens	Mutation(s): 0 Gene Names: cpe
UniProt
Find proteins for P01558 (Clostridium perfringens) Explore P01558 Go to UniProtKB: P01558
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01558
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
COP-2 antibody heavy chain	F [auth A], G [auth C], H [auth E]	260	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth D] SDF format, chain M [auth D] SDF format, chain N [auth I] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth C] SDF format, chain R [auth E] SDF format, chain S [auth E] SDF format, chain T [auth F] SDF format, chain U [auth F] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] MOL2 format, chain N [auth I] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth E] MOL2 format, chain S [auth E] MOL2 format, chain T [auth F] MOL2 format, chain U [auth F] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D] mmCIF format, chain N [auth I] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth E] mmCIF format, chain S [auth E] mmCIF format, chain T [auth F] mmCIF format, chain U [auth F]	J [auth B] K [auth B] L [auth D] M [auth D] N [auth I] J [auth B], K [auth B], L [auth D], M [auth D], N [auth I], O [auth A], P [auth A], Q [auth C], R [auth E], S [auth E], T [auth F], U [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth I] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth C] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth F] Interactions & Density Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth I] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth C] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.233 (Depositor), 0.236 (DCC)
R-Value Work: 0.182 (Depositor), 0.189 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.929	α = 90
b = 197.434	β = 109.54
c = 115.056	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
pointless	data scaling
PHASER	phasing
Coot	model building

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-02-12

Deposition Author(s):

Ogbu, C.P.

Kapoor, S.

Vecchio, A.J.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM138368
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM117372