5C7G

Crystal Structure of the b1 Domain of Human Neuropilin-1 in complex with a bicine molecule

PDB DOI: https://doi.org/10.2210/pdb5C7G/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-06-24 Released: 2016-07-06
Deposition Author(s): Didierjean, C., Jelsch, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.172
R-Value Work: 0.141
R-Value Observed: 0.143

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Design, synthesis and biological evaluation of new peptidomimetic compounds targeting NRP-1 receptor TO BE PUBLISHED

Richard, M., Pelligrini Moise, N., Jelsch, C., Maigret, B., Didierjean, C., Manival, X., Charron, C.

To be published.

Macromolecule Content

Total Structure Weight: 18.61 kDa
Atom Count: 1,528
Modelled Residue Count: 155
Deposited Residue Count: 161
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuropilin-1	A	161	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O14786
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BCN Query on BCN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	BICINE C₆ H₁₃ N O₄ FSVCELGFZIQNCK-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.172
R-Value Work: 0.141
R-Value Observed: 0.143
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.28	α = 90
b = 62.28	β = 90
c = 85.96	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
Coot	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-07-06

Deposition Author(s):

Didierjean, C.

Jelsch, C.

Revision History (Full details and data files)

Version 1.0: 2016-07-06
Type: Initial release
Version 2.0: 2024-01-10
Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description
Version 2.1: 2024-10-09
Changes: Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

5C7G

Crystal Structure of the b1 Domain of Human Neuropilin-1 in complex with a bicine molecule

Design, synthesis and biological evaluation of new peptidomimetic compounds targeting NRP-1 receptor TO BE PUBLISHED

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)