6Y41 | pdb_00006y41

Fibrinogen-like globe domain of human ANGPTL2

PDB DOI: https://doi.org/10.2210/pdb6Y41/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-02-19 Released: 2020-03-04
Deposition Author(s): Coker, J.A., Krojer, T., Mutisya, J.M., Arrowsmith, C.H., Bountra, C., Midwood, K.S., Yue, W.W., Marsden, B.D., Structural Genomics Consortium (SGC)
Funding Organization(s): Innovative Medicines Initiative

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.215 (Depositor), 0.216 (DCC)
R-Value Work:
0.192 (Depositor), 0.194 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Fibrinogen-like globe domain of human ANGPTL2

Coker, J.A., Krojer, T., Mutisya, J.M., Arrowsmith, C.H., Bountra, C., Midwood, K.S., Yue, W.W., Marsden, B.D., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 429.95 kDa
Atom Count: 31,544
Modeled Residue Count: 3,483
Deposited Residue Count: 3,632
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiopoietin-related protein 2	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	227	Homo sapiens	Mutation(s): 0 Gene Names: ANGPTL2, ARP2, UNQ170/PRO196
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKU9 (Homo sapiens) Explore Q9UKU9 Go to UniProtKB: Q9UKU9
PHAROS: Q9UKU9 GTEx: ENSG00000136859
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UKU9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain X [auth G] SDF format, chain Z [auth H] MOL2 format, chain X [auth G] MOL2 format, chain Z [auth H] mmCIF format, chain X [auth G] mmCIF format, chain Z [auth H]	X [auth G], Z [auth H]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain X [auth G] Focus chain Z [auth H] Interactions & Density Focus chain X [auth G] Focus chain Z [auth H]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain BA [auth I] SDF format, chain U [auth E] MOL2 format, chain BA [auth I] MOL2 format, chain U [auth E] mmCIF format, chain BA [auth I] mmCIF format, chain U [auth E]	BA [auth I], U [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth I] Focus chain U [auth E] Interactions & Density Focus chain BA [auth I] Focus chain U [auth E]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain CA [auth I] SDF format, chain DA [auth J] SDF format, chain EA [auth K] SDF format, chain FA [auth L] SDF format, chain GA [auth M] SDF format, chain HA [auth N] SDF format, chain IA [auth O] SDF format, chain JA [auth P] SDF format, chain Q [auth A] SDF format, chain R [auth B] SDF format, chain S [auth C] SDF format, chain T [auth D] SDF format, chain V [auth E] SDF format, chain W [auth F] SDF format, chain Y [auth G] MOL2 format, chain AA [auth H] MOL2 format, chain CA [auth I] MOL2 format, chain DA [auth J] MOL2 format, chain EA [auth K] MOL2 format, chain FA [auth L] MOL2 format, chain GA [auth M] MOL2 format, chain HA [auth N] MOL2 format, chain IA [auth O] MOL2 format, chain JA [auth P] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth D] MOL2 format, chain V [auth E] MOL2 format, chain W [auth F] MOL2 format, chain Y [auth G] mmCIF format, chain AA [auth H] mmCIF format, chain CA [auth I] mmCIF format, chain DA [auth J] mmCIF format, chain EA [auth K] mmCIF format, chain FA [auth L] mmCIF format, chain GA [auth M] mmCIF format, chain HA [auth N] mmCIF format, chain IA [auth O] mmCIF format, chain JA [auth P] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth D] mmCIF format, chain V [auth E] mmCIF format, chain W [auth F] mmCIF format, chain Y [auth G]	AA [auth H] CA [auth I] DA [auth J] EA [auth K] FA [auth L] AA [auth H], CA [auth I], DA [auth J], EA [auth K], FA [auth L], GA [auth M], HA [auth N], IA [auth O], JA [auth P], Q [auth A], R [auth B], S [auth C], T [auth D], V [auth E], W [auth F], Y [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain CA [auth I] Focus chain DA [auth J] Focus chain EA [auth K] Focus chain FA [auth L] Focus chain GA [auth M] Focus chain HA [auth N] Focus chain IA [auth O] Focus chain JA [auth P] Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain W [auth F] Focus chain Y [auth G] Interactions & Density Focus chain AA [auth H] Focus chain CA [auth I] Focus chain DA [auth J] Focus chain EA [auth K] Focus chain FA [auth L] Focus chain GA [auth M] Focus chain HA [auth N] Focus chain IA [auth O] Focus chain JA [auth P] Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain W [auth F] Focus chain Y [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.215 (Depositor), 0.216 (DCC)
R-Value Work: 0.192 (Depositor), 0.194 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.94	α = 90
b = 154.86	β = 90
c = 172.34	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-03-04

Deposition Author(s):

Structural Genomics Consortium (SGC)

Funding Organization	Location	Grant Number
Innovative Medicines Initiative	United Kingdom	115766

Revision History (Full details and data files)

Version 1.0: 2020-03-04
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary