4XLW

Complex of Notch1 (EGF11-13) bound to Delta-like 4 (N-EGF2)

PDB DOI: https://doi.org/10.2210/pdb4XLW/pdb

Classification: PROTEIN BINDING
Organism(s): Rattus norvegicus
Expression System: Trichoplusia ni
Mutation(s): Yes

Deposited: 2015-01-13 Released: 2015-03-04
Deposition Author(s): Luca, V.C., Jude, K.M., Garcia, K.C.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.39 Å
R-Value Free: 0.310
R-Value Work: 0.257
R-Value Observed: 0.260

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 175.25 kDa
Atom Count: 11,773
Modelled Residue Count: 1,496
Deposited Residue Count: 1,540
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neurogenic locus notch homolog protein 1	A, C, E, G	124	Rattus norvegicus	Mutation(s): 0 Gene Names: Notch1
UniProt
Find proteins for Q07008 (Rattus norvegicus) Explore Q07008 Go to UniProtKB: Q07008
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q07008
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Delta-like protein	B, D, F, H	261	Rattus norvegicus	Mutation(s): 4 Gene Names: Dll4, Dll4_predicted, rCG_26804
UniProt
Find proteins for D3ZHH1 (Rattus norvegicus) Explore D3ZHH1 Go to UniProtKB: D3ZHH1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D3ZHH1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain FA [auth F] SDF format, chain MA [auth H] SDF format, chain NA [auth H] SDF format, chain P [auth B] SDF format, chain X [auth D] SDF format, chain EA [auth F] MOL2 format, chain FA [auth F] MOL2 format, chain MA [auth H] MOL2 format, chain NA [auth H] MOL2 format, chain P [auth B] MOL2 format, chain X [auth D] MOL2 format, chain EA [auth F]	EA [auth F] FA [auth F] MA [auth H] NA [auth H] P [auth B] EA [auth F], FA [auth F], MA [auth H], NA [auth H], P [auth B], X [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain EA [auth F] Focus chain FA [auth F] Focus chain MA [auth H] Focus chain NA [auth H] Focus chain P [auth B] Focus chain X [auth D] Interactions & Density Focus chain EA [auth F] Focus chain FA [auth F] Focus chain MA [auth H] Focus chain NA [auth H] Focus chain P [auth B] Focus chain X [auth D]
BGC Query on BGC Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain IA [auth G] SDF format, chain KA [auth G] SDF format, chain L [auth A] SDF format, chain LA [auth G] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain Q [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] MOL2 format, chain AA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain IA [auth G] MOL2 format, chain KA [auth G] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth G] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C]	AA [auth E] CA [auth E] DA [auth E] IA [auth G] KA [auth G] AA [auth E], CA [auth E], DA [auth E], IA [auth G], KA [auth G], L [auth A], LA [auth G], N [auth A], O [auth A], Q [auth C], S [auth C], T [auth C]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain AA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain IA [auth G] Focus chain KA [auth G] Focus chain L [auth A] Focus chain LA [auth G] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth C] Focus chain S [auth C] Focus chain T [auth C] Interactions & Density Focus chain AA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain IA [auth G] Focus chain KA [auth G] Focus chain L [auth A] Focus chain LA [auth G] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth C] Focus chain S [auth C] Focus chain T [auth C]
FUC Query on FUC Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain JA [auth G] SDF format, chain M [auth A] SDF format, chain R [auth C] MOL2 format, chain BA [auth E] MOL2 format, chain JA [auth G] MOL2 format, chain M [auth A] MOL2 format, chain R [auth C]	BA [auth E], JA [auth G], M [auth A], R [auth C]	alpha-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-SXUWKVJYSA-N		Interactions Focus chain BA [auth E] Focus chain JA [auth G] Focus chain M [auth A] Focus chain R [auth C] Interactions & Density Focus chain BA [auth E] Focus chain JA [auth G] Focus chain M [auth A] Focus chain R [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain GA [auth G] SDF format, chain HA [auth G] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain Y [auth E] SDF format, chain Z [auth E] MOL2 format, chain GA [auth G] MOL2 format, chain HA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E]	GA [auth G] HA [auth G] I [auth A] J [auth A] K [auth A] GA [auth G], HA [auth G], I [auth A], J [auth A], K [auth A], U [auth C], V [auth C], W [auth C], Y [auth E], Z [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain GA [auth G] Focus chain HA [auth G] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain GA [auth G] Focus chain HA [auth G] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain Y [auth E] Focus chain Z [auth E]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY Query on MLY	B, D, F, H	L-PEPTIDE LINKING	C₈ H₁₈ N₂ O₂		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.39 Å
R-Value Free: 0.310
R-Value Work: 0.257
R-Value Observed: 0.260
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.15785/SBGRID/69

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.56	α = 90
b = 95.57	β = 96.21
c = 122.9	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2015-03-04

Deposition Author(s):

Luca, V.C.

Jude, K.M.

Garcia, K.C.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	NIH-1RO1-GM097015

Revision History (Full details and data files)

Version 1.0: 2015-03-04
Type: Initial release
Version 1.1: 2015-03-11
Changes: Database references
Version 1.2: 2015-05-27
Changes: Refinement description
Version 1.3: 2015-06-10
Changes: Refinement description
Version 1.4: 2017-09-20
Changes: Author supporting evidence, Derived calculations, Source and taxonomy
Version 1.5: 2019-12-25
Changes: Author supporting evidence, Data collection
Version 1.6: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary