6NDE

RHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN WITH PRASEDYMIUM

PDB DOI: https://doi.org/10.2210/pdb6NDE/pdb

Classification: CELL ADHESION/TOXIN
Organism(s): Calloselasma rhodostoma, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-12-13 Released: 2019-01-23
Deposition Author(s): Stetefeld, J., McDougall, M.D., Loewen, P.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.369
R-Value Work: 0.290
R-Value Observed: 0.294

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

RHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN WITH PRASEDYMIUM BOUND

Stetefeld, J., McDougall, M.D., Loewen, P.C.

To be published.

Macromolecule Content

Total Structure Weight: 328.89 kDa
Atom Count: 21,590
Modelled Residue Count: 2,664
Deposited Residue Count: 2,856
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Snaclec rhodocetin subunit gamma	A, D, G, J, M A, D, G, J, M, P	135	Calloselasma rhodostoma	Mutation(s): 0
UniProt
Find proteins for D2YW39 (Calloselasma rhodostoma) Explore D2YW39 Go to UniProtKB: D2YW39
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D2YW39
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Snaclec rhodocetin subunit delta	B, E, H, K, N B, E, H, K, N, Q	124	Calloselasma rhodostoma	Mutation(s): 0
UniProt
Find proteins for D2YW40 (Calloselasma rhodostoma) Explore D2YW40 Go to UniProtKB: D2YW40
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D2YW40
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-2	C, F, I, L, O C, F, I, L, O, R	217	Homo sapiens	Mutation(s): 0 Gene Names: ITGA2, CD49B
UniProt & NIH Common Fund Data Resources
Find proteins for P17301 (Homo sapiens) Explore P17301 Go to UniProtKB: P17301
PHAROS: P17301 GTEx: ENSG00000164171
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P17301
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PR Query on PR Download Ideal Coordinates CCD File SDF format, chain DA [auth F] SDF format, chain JA [auth I] SDF format, chain PA [auth L] SDF format, chain UA [auth O] SDF format, chain V [auth C] SDF format, chain ZA [auth R] MOL2 format, chain DA [auth F] MOL2 format, chain JA [auth I] MOL2 format, chain PA [auth L] MOL2 format, chain UA [auth O] MOL2 format, chain V [auth C] MOL2 format, chain ZA [auth R] mmCIF format, chain DA [auth F] mmCIF format, chain JA [auth I] mmCIF format, chain PA [auth L] mmCIF format, chain UA [auth O] mmCIF format, chain V [auth C] mmCIF format, chain ZA [auth R]	DA [auth F] JA [auth I] PA [auth L] UA [auth O] V [auth C] DA [auth F], JA [auth I], PA [auth L], UA [auth O], V [auth C], ZA [auth R]	PRASEODYMIUM ION Pr WCWKKSOQLQEJTE-UHFFFAOYSA-N		Interactions Focus chain DA [auth F] Focus chain JA [auth I] Focus chain PA [auth L] Focus chain UA [auth O] Focus chain V [auth C] Focus chain ZA [auth R]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain AB [auth R] SDF format, chain CA [auth E] SDF format, chain GA [auth G] SDF format, chain IA [auth H] SDF format, chain LA [auth J] SDF format, chain OA [auth K] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain TA [auth N] SDF format, chain U [auth B] SDF format, chain WA [auth O] SDF format, chain XA [auth Q] SDF format, chain Y [auth D] SDF format, chain YA [auth Q] MOL2 format, chain AA [auth E] MOL2 format, chain AB [auth R] MOL2 format, chain CA [auth E] MOL2 format, chain GA [auth G] MOL2 format, chain IA [auth H] MOL2 format, chain LA [auth J] MOL2 format, chain OA [auth K] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth N] MOL2 format, chain U [auth B] MOL2 format, chain WA [auth O] MOL2 format, chain XA [auth Q] MOL2 format, chain Y [auth D] MOL2 format, chain YA [auth Q] mmCIF format, chain AA [auth E] mmCIF format, chain AB [auth R] mmCIF format, chain CA [auth E] mmCIF format, chain GA [auth G] mmCIF format, chain IA [auth H] mmCIF format, chain LA [auth J] mmCIF format, chain OA [auth K] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth N] mmCIF format, chain U [auth B] mmCIF format, chain WA [auth O] mmCIF format, chain XA [auth Q] mmCIF format, chain Y [auth D] mmCIF format, chain YA [auth Q]	AA [auth E] AB [auth R] CA [auth E] GA [auth G] IA [auth H] AA [auth E], AB [auth R], CA [auth E], GA [auth G], IA [auth H], LA [auth J], OA [auth K], S [auth A], T [auth A], TA [auth N], U [auth B], WA [auth O], XA [auth Q], Y [auth D], YA [auth Q]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth E] Focus chain AB [auth R] Focus chain CA [auth E] Focus chain GA [auth G] Focus chain IA [auth H] Focus chain LA [auth J] Focus chain OA [auth K] Focus chain S [auth A] Focus chain T [auth A] Focus chain TA [auth N] Focus chain U [auth B] Focus chain WA [auth O] Focus chain XA [auth Q] Focus chain Y [auth D] Focus chain YA [auth Q]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain BB [auth R] SDF format, chain FA [auth G] SDF format, chain HA [auth H] SDF format, chain MA [auth J] SDF format, chain NA [auth K] SDF format, chain RA [auth L] SDF format, chain SA [auth M] SDF format, chain X [auth C] MOL2 format, chain BA [auth E] MOL2 format, chain BB [auth R] MOL2 format, chain FA [auth G] MOL2 format, chain HA [auth H] MOL2 format, chain MA [auth J] MOL2 format, chain NA [auth K] MOL2 format, chain RA [auth L] MOL2 format, chain SA [auth M] MOL2 format, chain X [auth C] mmCIF format, chain BA [auth E] mmCIF format, chain BB [auth R] mmCIF format, chain FA [auth G] mmCIF format, chain HA [auth H] mmCIF format, chain MA [auth J] mmCIF format, chain NA [auth K] mmCIF format, chain RA [auth L] mmCIF format, chain SA [auth M] mmCIF format, chain X [auth C]	BA [auth E] BB [auth R] FA [auth G] HA [auth H] MA [auth J] BA [auth E], BB [auth R], FA [auth G], HA [auth H], MA [auth J], NA [auth K], RA [auth L], SA [auth M], X [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth E] Focus chain BB [auth R] Focus chain FA [auth G] Focus chain HA [auth H] Focus chain MA [auth J] Focus chain NA [auth K] Focus chain RA [auth L] Focus chain SA [auth M] Focus chain X [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain CB [auth R] SDF format, chain EA [auth F] SDF format, chain KA [auth I] SDF format, chain QA [auth L] SDF format, chain VA [auth O] SDF format, chain W [auth C] MOL2 format, chain CB [auth R] MOL2 format, chain EA [auth F] MOL2 format, chain KA [auth I] MOL2 format, chain QA [auth L] MOL2 format, chain VA [auth O] MOL2 format, chain W [auth C] mmCIF format, chain CB [auth R] mmCIF format, chain EA [auth F] mmCIF format, chain KA [auth I] mmCIF format, chain QA [auth L] mmCIF format, chain VA [auth O] mmCIF format, chain W [auth C]	CB [auth R] EA [auth F] KA [auth I] QA [auth L] VA [auth O] CB [auth R], EA [auth F], KA [auth I], QA [auth L], VA [auth O], W [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain CB [auth R] Focus chain EA [auth F] Focus chain KA [auth I] Focus chain QA [auth L] Focus chain VA [auth O] Focus chain W [auth C]
NH4 Query on NH4 Download Ideal Coordinates CCD File SDF format, chain Z [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain Z [auth D]	Z [auth D]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.369
R-Value Work: 0.290
R-Value Observed: 0.294
Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.351	α = 90
b = 132.351	β = 90
c = 254.244	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2019-01-23

Deposition Author(s):

Stetefeld, J.

McDougall, M.D.

Loewen, P.C.

Revision History (Full details and data files)

Version 1.0: 2019-01-23
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary