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), 0.260 (DCC)
R-Value Work:
0.202 (Depositor), 0.200 (DCC)
R-Value Observed:
0.205 (Depositor)

wwPDB Validation 3D Report Full Report

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
Modelled Residue Count: 426
Deposited Residue Count: 445
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ipilimumab fab heavy chain	A [auth H]	230	Homo sapiens	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
ipilimumab fab light chain	B [auth L]	215	Homo sapiens	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
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth H] SDF format, chain E [auth H] SDF format, chain D [auth H] SDF format, chain F [auth L] MOL2 format, chain C [auth H] MOL2 format, chain E [auth H] MOL2 format, chain D [auth H] MOL2 format, chain F [auth L] mmCIF format, chain C [auth H] mmCIF format, chain E [auth H] mmCIF format, chain D [auth H] mmCIF format, chain F [auth L]	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), 0.260 (DCC)
R-Value Work: 0.202 (Depositor), 0.200 (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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2019-09-11

Deposition Author(s):

Heo, Y.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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Help and Resources

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Crystal structure of the Fab fragment of ipilimumab

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

Entity ID: 1

Entity Groups

Sequence Annotations

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Entity ID: 2