7AMR | pdb_00007amr

Crystal structure of the complex of the KFN mutant of Jovi-1 Fab with human TRBC1

PDB DOI: https://doi.org/10.2210/pdb7AMR/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli, Homo sapiens
Mutation(s): No

Deposited: 2020-10-09 Released: 2022-04-20
Deposition Author(s): Ferrari, M., Bulek, A., Bughda, R., Jha, R., Welin, M., Logan, D.T., Sewell, A., Onuoha, S., Pule, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.225 (Depositor), 0.230 (DCC)
R-Value Work:
0.179 (Depositor), 0.180 (DCC)
R-Value Observed:
0.182 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure-Guided Engineering of Immunotherapies Targeting TRBC1 and TRBC2 in T Cell Malignancies

Ferrari, M., Baldan, V., Wawrzyniecka, P., Bulek, A., Kinna, A., Ma, B., Bugda, R., Akbar, Z., Srivastava, S., Ghongane, P., Gannon, I., Robson, M., Sillibourne, J., Jha, R., Lim, W., Hopkins, J., Welin, M., Surade, S., Dyson, M., McCafferty, J., Cordoba, S., Thomas, S., Logan, D., Sewell, A., Maciocia, P., Onuoha, S., Pule, M.

(2022) Res Sq

DOI: https://doi.org/10.21203/rs.3.rs-1475171/v1

Macromolecule Content

Total Structure Weight: 99.34 kDa
Atom Count: 7,570
Modeled Residue Count: 880
Deposited Residue Count: 896
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Human T-cell receptor alpha chain	A	206	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Human T-cell receptor beta chain TRBC2	B	246	Homo sapiens	Mutation(s): 0
Entity Groups
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Human Jovi-1 Fab fragment, KFN mutant, heavy chain	C [auth H]	225	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Human Jovi-1 Fab fragment, KFN mutant, light chain	D [auth L]	219	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth L] SDF format, chain K [auth L] SDF format, chain L MOL2 format, chain G [auth L] MOL2 format, chain K [auth L] MOL2 format, chain L mmCIF format, chain G [auth L] mmCIF format, chain K [auth L] mmCIF format, chain L	G [auth L], K [auth L], L	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth L] Focus chain K [auth L] Focus chain L Interactions & Density Focus chain G [auth L] Focus chain K [auth L] Focus chain L
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth H] SDF format, chain H [auth L] SDF format, chain I [auth L] MOL2 format, chain E [auth H] MOL2 format, chain H [auth L] MOL2 format, chain I [auth L] mmCIF format, chain E [auth H] mmCIF format, chain H [auth L] mmCIF format, chain I [auth L]	E [auth H], H [auth L], I [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Focus chain H [auth L] Focus chain I [auth L] Interactions & Density Focus chain E [auth H] Focus chain H [auth L] Focus chain I [auth L]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth H] SDF format, chain J [auth L] MOL2 format, chain F [auth H] MOL2 format, chain J [auth L] mmCIF format, chain F [auth H] mmCIF format, chain J [auth L]	F [auth H], J [auth L]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth H] Focus chain J [auth L] Interactions & Density Focus chain F [auth H] Focus chain J [auth L]