6JC2 | pdb_00006jc2

Crystal structure of the Fab fragment of ipilimumab

PDB DOI: https://doi.org/10.2210/pdb6JC2/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
Mutation(s): No

Deposited: 2019-01-27 Released: 2019-09-11
Deposition Author(s): Heo, Y.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.263 (Depositor), 0.263 (DCC)
R-Value Work:
0.202 (Depositor), 0.202 (DCC)
R-Value Observed:
0.205 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6JC2

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of the Fab Fragment of an Anti-CTLA-4 Antibody, Ipilimumab, Used for Cancer Immunotherapy

Lee, J.Y., Lee, H.T., Lee, S.H., Lim, H., Heo, Y.S.

(2019) Bull Korean Chem Soc 40: 582-585

DOI: https://doi.org/10.1002/bkcs.11712

Macromolecule Content

Total Structure Weight: 48.76 kDa
Atom Count: 3,311
Modeled Residue Count: 426
Deposited Residue Count: 445
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ipilimumab fab heavy chain	A [auth H]	230	Homo sapiens	Mutation(s): 0

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ipilimumab fab light chain	B [auth L]	215	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth H] SDF format, chain D [auth H] SDF format, chain F [auth L] SDF format, chain E [auth H] MOL2 format, chain C [auth H] MOL2 format, chain D [auth H] MOL2 format, chain F [auth L] MOL2 format, chain E [auth H] mmCIF format, chain C [auth H] mmCIF format, chain D [auth H] mmCIF format, chain F [auth L] mmCIF format, chain E [auth H]	C [auth H], D [auth H], E [auth H], F [auth L]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth H] Focus chain D [auth H] Focus chain E [auth H] Focus chain F [auth L] Interactions & Density Focus chain C [auth H] Focus chain D [auth H] Focus chain E [auth H] Focus chain F [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.263 (Depositor), 0.263 (DCC)
R-Value Work: 0.202 (Depositor), 0.202 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.614	α = 90
b = 119.614	β = 90
c = 82.597	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-09-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-09-11
Type: Initial release
Version 1.1: 2024-10-16
Changes: Data collection, Database references, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.