1CX8

CRYSTAL STRUCTURE OF THE ECTODOMAIN OF HUMAN TRANSFERRIN RECEPTOR

PDB DOI: https://doi.org/10.2210/pdb1CX8/pdb

Classification: METAL TRANSPORT
Organism(s): Homo sapiens
Expression System: Cricetinae gen. sp.
Mutation(s): No

Deposited: 1999-08-28 Released: 1999-09-09
Deposition Author(s): Lawrence, C.M., Ray, S., Babyonyshev, M., Galluser, R., Borhani, D., Harrison, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.284
R-Value Work: 0.243

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 581.9 kDa
Atom Count: 40,808
Modelled Residue Count: 5,112
Deposited Residue Count: 5,112
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRANSFERRIN RECEPTOR PROTEIN	A, B, C, D, E A, B, C, D, E, F, G, H	639	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P02786 (Homo sapiens) Explore P02786 Go to UniProtKB: P02786
PHAROS: P02786 GTEx: ENSG00000072274
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02786
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain AB [auth H] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain GA [auth E] SDF format, chain HA [auth E] SDF format, chain I [auth A] SDF format, chain IA [auth E] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain MA [auth F] SDF format, chain NA [auth F] SDF format, chain O [auth B] SDF format, chain OA [auth F] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain SA [auth G] SDF format, chain TA [auth G] SDF format, chain U [auth C] SDF format, chain UA [auth G] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain YA [auth H] SDF format, chain ZA [auth H] MOL2 format, chain AA [auth D] MOL2 format, chain AB [auth H] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain HA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain NA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain SA [auth G] MOL2 format, chain TA [auth G] MOL2 format, chain U [auth C] MOL2 format, chain UA [auth G] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain YA [auth H] MOL2 format, chain ZA [auth H]	AA [auth D] AB [auth H] BA [auth D] CA [auth D] GA [auth E] AA [auth D], AB [auth H], BA [auth D], CA [auth D], GA [auth E], HA [auth E], I [auth A], IA [auth E], J [auth A], K [auth A], MA [auth F], NA [auth F], O [auth B], OA [auth F], P [auth B], Q [auth B], SA [auth G], TA [auth G], U [auth C], UA [auth G], V [auth C], W [auth C], YA [auth H], ZA [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth D] Focus chain AB [auth H] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain MA [auth F] Focus chain NA [auth F] Focus chain O [auth B] Focus chain OA [auth F] Focus chain P [auth B] Focus chain Q [auth B] Focus chain SA [auth G] Focus chain TA [auth G] Focus chain U [auth C] Focus chain UA [auth G] Focus chain V [auth C] Focus chain W [auth C] Focus chain YA [auth H] Focus chain ZA [auth H] Interactions & Density Focus chain AA [auth D] Focus chain AB [auth H] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain MA [auth F] Focus chain NA [auth F] Focus chain O [auth B] Focus chain OA [auth F] Focus chain P [auth B] Focus chain Q [auth B] Focus chain SA [auth G] Focus chain TA [auth G] Focus chain U [auth C] Focus chain UA [auth G] Focus chain V [auth C] Focus chain W [auth C] Focus chain YA [auth H] Focus chain ZA [auth H]
SM Query on SM Download Ideal Coordinates CCD File SDF format, chain BB [auth H] SDF format, chain CB [auth H] SDF format, chain DA [auth D] SDF format, chain DB [auth H] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain JA [auth E] SDF format, chain KA [auth E] SDF format, chain L [auth A] SDF format, chain LA [auth E] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain PA [auth F] SDF format, chain QA [auth F] SDF format, chain R [auth B] SDF format, chain RA [auth F] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain VA [auth G] SDF format, chain WA [auth G] SDF format, chain X [auth C] SDF format, chain XA [auth G] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain BB [auth H] MOL2 format, chain CB [auth H] MOL2 format, chain DA [auth D] MOL2 format, chain DB [auth H] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain JA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain PA [auth F] MOL2 format, chain QA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain VA [auth G] MOL2 format, chain WA [auth G] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth G] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C]	BB [auth H] CB [auth H] DA [auth D] DB [auth H] EA [auth D] BB [auth H], CB [auth H], DA [auth D], DB [auth H], EA [auth D], FA [auth D], JA [auth E], KA [auth E], L [auth A], LA [auth E], M [auth A], N [auth A], PA [auth F], QA [auth F], R [auth B], RA [auth F], S [auth B], T [auth B], VA [auth G], WA [auth G], X [auth C], XA [auth G], Y [auth C], Z [auth C]	SAMARIUM (III) ION Sm DOSGOCSVHPUUIA-UHFFFAOYSA-N		Interactions Focus chain BB [auth H] Focus chain CB [auth H] Focus chain DA [auth D] Focus chain DB [auth H] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain PA [auth F] Focus chain QA [auth F] Focus chain R [auth B] Focus chain RA [auth F] Focus chain S [auth B] Focus chain T [auth B] Focus chain VA [auth G] Focus chain WA [auth G] Focus chain X [auth C] Focus chain XA [auth G] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain BB [auth H] Focus chain CB [auth H] Focus chain DA [auth D] Focus chain DB [auth H] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain PA [auth F] Focus chain QA [auth F] Focus chain R [auth B] Focus chain RA [auth F] Focus chain S [auth B] Focus chain T [auth B] Focus chain VA [auth G] Focus chain WA [auth G] Focus chain X [auth C] Focus chain XA [auth G] Focus chain Y [auth C] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.284
R-Value Work: 0.243
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.4	α = 90
b = 216.9	β = 90
c = 361.9	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
DM	model building
CNS	refinement
DM	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 1999-09-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1999-09-09
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2016-12-14
Changes: Structure summary
Version 1.4: 2018-01-31
Changes: Experimental preparation
Version 1.5: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary