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

Starting Model: experimental
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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. [email protected]

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
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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
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain C [auth X]	Go to GlyGen: P35968-1
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] mmCIF 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 E [auth H] SDF format, chain F [auth H] SDF format, chain G [auth L] SDF format, chain H [auth L] SDF format, chain J [auth X] SDF format, chain K [auth X] MOL2 format, chain E [auth H] MOL2 format, chain F [auth H] MOL2 format, chain G [auth L] MOL2 format, chain H [auth L] MOL2 format, chain J [auth X] MOL2 format, chain K [auth X] mmCIF format, chain E [auth H] mmCIF format, chain F [auth H] mmCIF format, chain G [auth L] mmCIF format, chain H [auth L] mmCIF format, chain J [auth X] mmCIF format, chain K [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