4RN5 | pdb_00004rn5

B1 domain of human Neuropilin-1 with acetate ion in a ligand-binding site

PDB DOI: https://doi.org/10.2210/pdb4RN5/pdb

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

Deposited: 2014-10-23 Released: 2015-10-28
Deposition Author(s): Allerston, C.K., Yelland, T.S., Jarvis, A., Jenkins, K., Winfield, N., Cheng, L., Jia, H., Zachary, I., Selwood, D.L., Djordjevic, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free:
0.201 (Depositor), 0.196 (DCC)
R-Value Work:
0.176 (Depositor), 0.175 (DCC)
R-Value Observed:
0.178 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Conserved water molecules in a ligand-binding site of neuropilin-1

Allerston, C.K., Yelland, T.S., Jarvis, A., Jenkins, K., Winfield, N., Cheng, L., Jia, H., Zachary, I., Selwood, D.L., Djordjevic, S.

To be published.

Macromolecule Content

Total Structure Weight: 18.2 kDa
Atom Count: 1,432
Modeled Residue Count: 158
Deposited Residue Count: 158
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuropilin-1	A	158	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
ACT Query on ACT 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]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.201 (Depositor), 0.196 (DCC)
R-Value Work: 0.176 (Depositor), 0.175 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.839	α = 90
b = 62.839	β = 90
c = 87.918	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
PHENIX	refinement
d*TREK	data reduction
SCALA	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-10-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-10-28
Type: Initial release
Version 1.1: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary

4RN5 | pdb_00004rn5

B1 domain of human Neuropilin-1 with acetate ion in a ligand-binding site

Literature

Conserved water molecules in a ligand-binding site of neuropilin-1

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand