4IUA

Crystal Structure of the NK2 Fragment (31-290) of the mouse Hepatocyte Growth Factor/Scatter Factor

PDB DOI: https://doi.org/10.2210/pdb4IUA/pdb

Classification: HORMONE
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2013-01-20 Released: 2013-02-13
Deposition Author(s): Tolbert, W.D., Zhou, E., Kovach, A., Melcher, K., Xu, H.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.05 Å
R-Value Free: 0.245
R-Value Work: 0.176
R-Value Observed: 0.183

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of the NK2 Fragment of the mouse Hepatocyte Growth Factor/Scatter Factor

Tolbert, W.D., Zhou, E., Kovach, A., Melcher, K., Xu, H.E.

To be published.

Macromolecule Content

Total Structure Weight: 247.14 kDa
Atom Count: 16,628
Modelled Residue Count: 2,016
Deposited Residue Count: 2,096
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor	A, B, C, D, E A, B, C, D, E, F, G, H	262	Mus musculus	Mutation(s): 1 Gene Names: Hgf
UniProt
Find proteins for Q08048 (Mus musculus) Explore Q08048 Go to UniProtKB: Q08048
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q08048
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain FA [auth H] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain T [auth D] SDF format, chain X [auth E] SDF format, chain Y [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain T [auth D] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth F]	CA [auth G] FA [auth H] I [auth A] L [auth B] P [auth B] CA [auth G], FA [auth H], I [auth A], L [auth B], P [auth B], Q [auth C], R [auth C], T [auth D], X [auth E], Y [auth F]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain CA [auth G] Focus chain FA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth D] Focus chain X [auth E] Focus chain Y [auth F] Interactions & Density Focus chain CA [auth G] Focus chain FA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth D] Focus chain X [auth E] Focus chain Y [auth F]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain BA [auth F] SDF format, chain DA [auth G] SDF format, chain EA [auth G] SDF format, chain GA [auth H] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain Z [auth F] MOL2 format, chain AA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain DA [auth G] MOL2 format, chain EA [auth G] MOL2 format, chain GA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain Z [auth F]	AA [auth F] BA [auth F] DA [auth G] EA [auth G] GA [auth H] AA [auth F], BA [auth F], DA [auth G], EA [auth G], GA [auth H], J [auth A], K [auth A], M [auth B], N [auth B], O [auth B], S [auth C], U [auth D], V [auth D], W [auth D], Z [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain GA [auth H] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain GA [auth H] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.05 Å
R-Value Free: 0.245
R-Value Work: 0.176
R-Value Observed: 0.183
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.62	α = 90
b = 127.328	β = 90.25
c = 129.6	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CNS	refinement
PHENIX	model building
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing
PHENIX	phasing
HKL-2000	data collection

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-02-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-02-13
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2019-07-17
Changes: Data collection, Refinement description
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description