7KF1

Crystal structure of bH1 Fab variant (CDR H3 loop design 14_0130) in complex with VEGF

PDB DOI: https://doi.org/10.2210/pdb7KF1/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Cricetulus griseus, Homo sapiens
Mutation(s): No

Deposited: 2020-10-13 Released: 2021-11-10
Deposition Author(s): Shi, R., Picard, M.-E., Manenda, M.S.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.232
R-Value Work: 0.189
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of bH1 Fab CDR H3 loop variants in apo form and in complex with VEGF

Picard, M.-E., Manenda, M.S., Corbeil, C., Sulea, T., Baardsness, J., Hogues, H., Gaudreault, F., Deprez, C., Purisima, E.O., Shi, R.

To be published.

Macromolecule Content

Total Structure Weight: 252.04 kDa
Atom Count: 17,155
Modelled Residue Count: 2,118
Deposited Residue Count: 2,284
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-VEGF-A Fab bH1 heavy chain	A [auth H], D [auth A], G [auth D], J [auth G]	237	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-VEGF-A Fab bH1 light chain	B [auth L], E [auth B], H [auth E], K [auth I]	218	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform L-VEGF206 of Vascular endothelial growth factor A	C [auth V], F [auth C], I [auth F], L [auth J]	116	Homo sapiens	Mutation(s): 0 Gene Names: VEGFA, VEGF
UniProt & NIH Common Fund Data Resources
Find proteins for P15692 (Homo sapiens) Explore P15692 Go to UniProtKB: P15692
PHAROS: P15692 GTEx: ENSG00000112715
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15692
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain M [auth H] SDF format, chain N [auth H] SDF format, chain O [auth H] SDF format, chain P [auth L] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain W [auth G] SDF format, chain X [auth G] MOL2 format, chain M [auth H] MOL2 format, chain N [auth H] MOL2 format, chain O [auth H] MOL2 format, chain P [auth L] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain W [auth G] MOL2 format, chain X [auth G]	M [auth H] N [auth H] O [auth H] P [auth L] Q [auth A] M [auth H], N [auth H], O [auth H], P [auth L], Q [auth A], R [auth A], S [auth A], T [auth D], U [auth D], V [auth D], W [auth G], X [auth G]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth H] Focus chain N [auth H] Focus chain O [auth H] Focus chain P [auth L] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth G] Focus chain X [auth G] Interactions & Density Focus chain M [auth H] Focus chain N [auth H] Focus chain O [auth H] Focus chain P [auth L] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth G] Focus chain X [auth G]