1LQV

Crystal structure of the Endothelial protein C receptor with phospholipid in the groove in complex with Gla domain of protein C.

PDB DOI: https://doi.org/10.2210/pdb1LQV/pdb

Classification: BLOOD CLOTTING
Organism(s): Homo sapiens
Expression System: Cricetulus griseus
Mutation(s): Yes
Membrane Protein: Yes OPM

Deposited: 2002-05-13 Released: 2002-06-19
Deposition Author(s): Oganesyan, V., Oganesyan, N., Terzyan, S., Dongfeng, Q., Dauter, Z., Esmon, N.L., Esmon, C.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.222
R-Value Work: 0.189
R-Value Observed: 0.189

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 56.17 kDa
Atom Count: 4,048
Modelled Residue Count: 411
Deposited Residue Count: 452
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endothelial protein C receptor	A, B	193	Homo sapiens	Mutation(s): 0 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNN8 (Homo sapiens) Explore Q9UNN8 Go to UniProtKB: Q9UNN8
PHAROS: Q9UNN8 GTEx: ENSG00000101000
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UNN8
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin-K dependent protein C	C, D	33	Homo sapiens	Mutation(s): 9 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P04070 (Homo sapiens) Explore P04070 Go to UniProtKB: P04070
PHAROS: P04070 GTEx: ENSG00000115718
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04070
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PTY Query on PTY Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B]	H [auth A], L [auth B]	PHOSPHATIDYLETHANOLAMINE C₄₀ H₈₀ N O₈ P NJGIRBISCGPRPF-KXQOOQHDSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain H [auth A] Focus chain L [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain K [auth B] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B]	E [auth A] F [auth A] G [auth A] I [auth B] J [auth B] E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain Y [auth D] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain X [auth D] SDF format, chain Z [auth D] MOL2 format, chain M [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth D]	M [auth C] N [auth C] O [auth C] P [auth C] Q [auth C] M [auth C], N [auth C], O [auth C], P [auth C], Q [auth C], R [auth C], S [auth C], T [auth D], U [auth D], V [auth D], W [auth D], X [auth D], Y [auth D], Z [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CGU Query on CGU	C, D	L-PEPTIDE LINKING	C₆ H₉ N O₆		GLU

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.222
R-Value Work: 0.189
R-Value Observed: 0.189
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.22	α = 90
b = 62.36	β = 101.81
c = 71.03	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2002-06-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2002-06-19
Type: Initial release
Version 1.1: 2008-04-28
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-04-03
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

1LQV

Crystal structure of the Endothelial protein C receptor with phospholipid in the groove in complex with Gla domain of protein C.

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2