8UWZ | pdb_00008uwz

The structure of Raamsizumab in complex with VEGF121

• PDB DOI: https://doi.org/10.2210/pdb8UWZ/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-11-08 Released: 2024-11-13 
• Deposition Author(s): Singer, A.U., Bruce, H., Blazer, L., Sicheri, F., Adams, J.J., Sidhu, S.S.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.298 (Depositor), 0.298 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.237 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Starting Models: experimental

Literature

Raamsizumab: A Potent Synthetic Human Anti-VEGF Neutralizing Fab for Treatment of Ocular Neovascularization Diseases

Fellouse, F.A., Harit, R.K., Arun, S., Arora, R., Wagner, N., Antony, A., Wong, S., Yang, N., Rajakrishnan, S., Anthony, M., Gokul, S., Vinodh, S., Bhunia, S., Vinothini, T.M., Choubey, S., Rajendran, A., Srivastava, A., Seshagiri, S., Gross, M.L., Leung, D.W., Amarasinghe, G.K., Chaudhuri, A., Sidhu, S.S., Ramchand, C.N.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 125.13 kDa 
• Atom Count: 7,733 
• Modeled Residue Count: 1,047 
• Deposited Residue Count: 1,122 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Raamsizumab heavy chain	A [auth C], E [auth A]	228	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Raamsizumab light chain S1C variant	B [auth D], F [auth B]	212	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform VEGF121 of Vascular endothelial growth factor A, long form	C [auth E], D [auth F]	121	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P15692 (Homo sapiens) Explore P15692  Go to UniProtKB:  P15692
PHAROS:  P15692 GTEx:  ENSG00000112715
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P15692-13

Oligosaccharides

Help  

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.298 (Depositor), 0.298 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.237 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.747	α = 90
b = 167.747	β = 90
c = 42.501	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-11-13 
Deposition Author(s): Singer, A.U., Bruce, H., Blazer, L., Sicheri, F., Adams, J.J., Sidhu, S.S.

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Funding Organization	Location	Grant Number
Other private	India	--

Revision History  

• Version 1.0: 2024-11-13
  Type: Initial release