1GMO

CRYSTAL STRUCTURES OF NK1-HEPARIN COMPLEXES REVEAL THE BASIS FOR NK1 ACTIVITY AND ENABLE ENGINEERING OF POTENT AGONISTS OF THE MET RECEPTOR

PDB DOI: https://doi.org/10.2210/pdb1GMO/pdb

Classification: HORMONE
Organism(s): Homo sapiens
Expression System: Komagataella phaffii GS115
Mutation(s): Yes

Deposited: 2001-09-20 Released: 2001-10-02
Deposition Author(s): Lietha, D., Chirgadze, D.Y., Mulloy, B., Blundell, T.L., Gherardi, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.295
R-Value Work: 0.254
R-Value Observed: 0.254

wwPDB Validation 3D Report Full Report

This is version 3.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 184.3 kDa
Atom Count: 11,555
Modelled Residue Count: 1,377
Deposited Residue Count: 1,464
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	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14210
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid	I	6		N/A	Interactions Focus chain I Interactions & Density Focus chain I
Glycosylation Resources
GlyTouCan: G82873VJ GlyCosmos: G82873VJ

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid	J	7		N/A	Interactions Focus chain J Interactions & Density Focus chain J
Glycosylation Resources
GlyTouCan: G07892WL GlyCosmos: G07892WL

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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-(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	K	8		N/A	Interactions Focus chain K Interactions & Density Focus chain K
Glycosylation Resources
GlyTouCan: G22032RS GlyCosmos: G22032RS

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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-(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	L	9		N/A	Interactions Focus chain L Interactions & Density Focus chain L
Glycosylation Resources
GlyTouCan: G10608JX GlyCosmos: G10608JX

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	M, N	6		N/A	Interactions Focus chain M Focus chain N Interactions & Density Focus chain M Focus chain N
Glycosylation Resources
GlyTouCan: G30141AL GlyCosmos: G30141AL

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 AA [auth F] SDF format, chain BA [auth G] SDF format, chain DA [auth H] SDF format, chain P [auth A] SDF format, chain R [auth B] SDF format, chain T [auth C] SDF format, chain V [auth D] SDF format, chain X [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain BA [auth G] MOL2 format, chain DA [auth H] MOL2 format, chain P [auth A] MOL2 format, chain R [auth B] MOL2 format, chain T [auth C] MOL2 format, chain V [auth D] MOL2 format, chain X [auth E]	AA [auth F] BA [auth G] DA [auth H] P [auth A] R [auth B] AA [auth F], BA [auth G], DA [auth H], P [auth A], R [auth B], T [auth C], V [auth D], X [auth E]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth G] Focus chain DA [auth H] Focus chain P [auth A] Focus chain R [auth B] Focus chain T [auth C] Focus chain V [auth D] Focus chain X [auth E] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth G] Focus chain DA [auth H] Focus chain P [auth A] Focus chain R [auth B] Focus chain T [auth C] Focus chain V [auth D] Focus chain X [auth E]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain CA [auth H] SDF format, chain O [auth A] SDF format, chain Q [auth B] SDF format, chain S [auth C] SDF format, chain U [auth D] SDF format, chain W [auth E] SDF format, chain Y [auth F] SDF format, chain Z [auth F] MOL2 format, chain CA [auth H] MOL2 format, chain O [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth C] MOL2 format, chain U [auth D] MOL2 format, chain W [auth E] MOL2 format, chain Y [auth F] MOL2 format, chain Z [auth F]	CA [auth H] O [auth A] Q [auth B] S [auth C] U [auth D] CA [auth H], O [auth A], Q [auth B], S [auth C], U [auth D], W [auth E], Y [auth F], Z [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CA [auth H] Focus chain O [auth A] Focus chain Q [auth B] Focus chain S [auth C] Focus chain U [auth D] Focus chain W [auth E] Focus chain Y [auth F] Focus chain Z [auth F] Interactions & Density Focus chain CA [auth H] Focus chain O [auth A] Focus chain Q [auth B] Focus chain S [auth C] Focus chain U [auth D] Focus chain W [auth E] Focus chain Y [auth F] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.295
R-Value Work: 0.254
R-Value Observed: 0.254
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.7	α = 90
b = 174.1	β = 90
c = 59.9	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2001-10-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2001-10-02
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 2.0: 2017-07-12
Changes: Advisory, Atomic model, Derived calculations
Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 3.1: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary