8C5G | pdb_00008c5g

Structure of human Neuropilin-1 b1b2 domains in complex with Chlorotoxin (Leiurus quinquestriatus)

PDB DOI: https://doi.org/10.2210/pdb8C5G/pdb

Classification: TOXIN
Organism(s): Homo sapiens, Leiurus quinquestriatus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-01-09 Released: 2024-01-17
Deposition Author(s): Boros, E., Ecsedi, P., Szakacs, D., Nyitray, L.
Funding Organization(s): National Research Development and Innovation Office (NKFIH)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.314 (Depositor), 0.317 (DCC)
R-Value Work:
0.263 (Depositor), 0.268 (DCC)
R-Value Observed:
0.265 (Depositor)

Starting Models: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Structure of human Neuropilin-1 b1b2 domains in complex with Chlorotoxin (Leiurus quinquestriatus)

Boros, E., Ecsedi, P., Szakacs, D., Nyitray, L.

To be published.

Macromolecule Content

Total Structure Weight: 79.84 kDa
Atom Count: 5,195
Modeled Residue Count: 666
Deposited Residue Count: 704
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuropilin-1	A, D [auth B]	316	Homo sapiens	Mutation(s): 0 Gene Names: NRP1, NRP, VEGF165R
UniProt & NIH Common Fund Data Resources
Find proteins for O14786 (Homo sapiens) Explore O14786 Go to UniProtKB: O14786
PHAROS: O14786 GTEx: ENSG00000099250
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O14786
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorotoxin	B [auth D], C	36	Leiurus quinquestriatus	Mutation(s): 0
UniProt
Find proteins for P45639 (Leiurus quinquestriatus quinquestriatus) Explore P45639 Go to UniProtKB: P45639
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P45639
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.314 (Depositor), 0.317 (DCC)
R-Value Work: 0.263 (Depositor), 0.268 (DCC)
R-Value Observed: 0.265 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.88	α = 90
b = 194.45	β = 92.33
c = 74.05	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-01-17

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Development and Innovation Office (NKFIH)	Hungary	2018-1.2-1-NKP

Revision History (Full details and data files)

Version 1.0: 2024-01-17
Type: Initial release
Version 1.1: 2024-11-13
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.