4IUA | pdb_00004iua

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 (Depositor), 0.250 (DCC)
R-Value Work:
0.176 (Depositor), 0.180 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 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
Modeled Residue Count: 2,016
Deposited Residue Count: 2,096
Unique protein chains: 1

Macromolecules

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(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] mmCIF format, chain CA [auth G] mmCIF format, chain FA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain T [auth D] mmCIF format, chain X [auth E] mmCIF 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 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] SDF format, chain N [auth B] 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 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] MOL2 format, chain N [auth B] mmCIF format, chain AA [auth F] mmCIF format, chain BA [auth F] mmCIF format, chain DA [auth G] mmCIF format, chain EA [auth G] mmCIF format, chain GA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain O [auth B] mmCIF format, chain S [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain Z [auth F] mmCIF format, chain N [auth B]	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 (Depositor), 0.250 (DCC)
R-Value Work: 0.176 (Depositor), 0.180 (DCC)
R-Value Observed: 0.183 (Depositor)

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

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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
Version 1.4: 2024-11-06
Changes: Structure summary