3S35

Structural basis for the function of two anti-VEGF receptor antibodies

PDB DOI: https://doi.org/10.2210/pdb3S35/pdb

Classification: IMMUNE SYSTEM/Transferase
Organism(s): Mus musculus, Homo sapiens
Expression System: Homo sapiens, Spodoptera frugiperda
Mutation(s): No

Deposited: 2011-05-17 Released: 2011-08-24
Deposition Author(s): Franklin, M.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.259
R-Value Work: 0.203
R-Value Observed: 0.206

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

The Structural Basis for the Function of Two Anti-VEGF Receptor 2 Antibodies.

Franklin, M.C., Navarro, E.C., Wang, Y., Patel, S., Singh, P., Zhang, Y., Persaud, K., Bari, A., Griffith, H., Shen, L., Balderes, P., Kussie, P.

(2011) Structure 19: 1097-1107

PubMed: 21827946 Search on PubMed
DOI: https://doi.org/10.1016/j.str.2011.01.019
Primary Citation of Related Structures:
3S34, 3S35, 3S36, 3S37

PubMed Abstract:
The anti-VEGF receptor 2 antibody IMC-1121B is a promising antiangiogenic drug being tested for treatment of breast and gastric cancer. We have determined the structure of the 1121B Fab fragment in complex with domain 3 of VEGFR2, as well as the structure of a different neutralizing anti-VEGFR2 antibody, 6.64, also in complex with VEGFR2 domain 3. The two Fab fragments bind at opposite ends of VEGFR2 domain 3; 1121B directly blocks VEGF binding, whereas 6.64 may prevent receptor dimerization by perturbing the domain 3:domain 4 interface. Mutagenesis reveals that residues essential for VEGF, 1121B, and 6.64 binding are nonoverlapping among the three contact patches.

Organizational Affiliation

Department of Immunology, ImClone Systems, New York, NY 10014, USA. mfranklin@nysbc.org

Macromolecule Content

Total Structure Weight: 61.94 kDa
Atom Count: 4,610
Modelled Residue Count: 540
Deposited Residue Count: 556
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6.64 Fab heavy chain	A [auth H]	217	Mus musculus, Homo sapiens This entity is chimeric	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
6.64 Fab light chain	B [auth L]	217	Mus musculus, Homo sapiens This entity is chimeric	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Vascular endothelial growth factor receptor 2	C [auth X]	122	Homo sapiens	Mutation(s): 0 Gene Names: KDR, FLK1 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P35968 (Homo sapiens) Explore P35968 Go to UniProtKB: P35968
PHAROS: P35968 GTEx: ENSG00000128052
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P35968
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth A]	2		N-Glycosylation	Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain I [auth X] MOL2 format, chain I [auth X]	I [auth X]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth X] Interactions & Density Focus chain I [auth X]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth L] SDF format, chain K [auth X] SDF format, chain E [auth H] SDF format, chain F [auth H] SDF format, chain H [auth L] SDF format, chain J [auth X] MOL2 format, chain G [auth L] MOL2 format, chain K [auth X] MOL2 format, chain E [auth H] MOL2 format, chain F [auth H] MOL2 format, chain H [auth L] MOL2 format, chain J [auth X]	E [auth H] F [auth H] G [auth L] H [auth L] J [auth X] E [auth H], F [auth H], G [auth L], H [auth L], J [auth X], K [auth X]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth L] Focus chain H [auth L] Focus chain J [auth X] Focus chain K [auth X] Interactions & Density Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth L] Focus chain H [auth L] Focus chain J [auth X] Focus chain K [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.259
R-Value Work: 0.203
R-Value Observed: 0.206
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.937	α = 90
b = 112.13	β = 90
c = 156.971	γ = 90

Software Package:

Software Name	Purpose
APS	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-08-24

Deposition Author(s):

Franklin, M.C.

Revision History (Full details and data files)

Version 1.0: 2011-08-24
Type: Initial release
Version 1.1: 2017-11-08
Changes: Source and taxonomy
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary