3MKP | pdb_00003mkp

Crystal structure of 1K1 mutant of Hepatocyte Growth Factor/Scatter Factor fragment NK1 in complex with heparin

PDB DOI: https://doi.org/10.2210/pdb3MKP/pdb

Classification: HORMONE
Organism(s): Homo sapiens
Expression System: Komagataella pastoris
Mutation(s): Yes

Deposited: 2010-04-15 Released: 2010-08-18
Deposition Author(s): Gherardi, E., Chirgadze, D.Y., Blundell, T.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free:
0.261 (Depositor), 0.263 (DCC)
R-Value Work:
0.199 (Depositor)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Engineering a fragment of Hepatocyte Growth Factor/Scatter Factor for tissue and organ regeneration

Gherardi, E., Chirgadze, D.Y., Bocci, M., Brocchieri, C., Bevan, D., Kajstura, J., Esposito, G., Lietha, D., Rota, M., Leri, A., Mallorqui-Fernandez, N., Bandyopadhyay, A., Youles, M., Mulloy, B., Rowe, A., Alison, M., Edwards, D., Vannini, V., Blundell, T., Anversa, P.

To be published.

Macromolecule Content

Total Structure Weight: 87.89 kDa
Atom Count: 5,766
Modeled Residue Count: 688
Deposited Residue Count: 732
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor	A, B, C, D	183	Homo sapiens	Mutation(s): 2
UniProt & NIH Common Fund Data Resources
Find proteins for P14210 (Homo sapiens) Explore P14210 Go to UniProtKB: P14210
PHAROS: P14210 GTEx: ENSG00000019991
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14210
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose	E	6		N/A	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G30141AL GlyCosmos: G30141AL

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SGN Query on SGN Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose C₆ H₁₃ N O₁₁ S₂ DQTRACMFIGDHSN-UKFBFLRUSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain N [auth D] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain N [auth D] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A], J [auth B], L [auth C], N [auth D]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B], K [auth C], M [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free: 0.261 (Depositor), 0.263 (DCC)
R-Value Work: 0.199 (Depositor)
R-Value Observed: 0.202 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.73	α = 90
b = 129.73	β = 90
c = 118.19	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-08-18

Deposition Author(s):

Gherardi, E.

Chirgadze, D.Y.

Blundell, T.L.

Revision History (Full details and data files)

Version 1.0: 2010-08-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-11-13
Changes: Structure summary