6JAS

Human serum transferrin with iron citrate bound

PDB DOI: https://doi.org/10.2210/pdb6JAS/pdb

Classification: METAL TRANSPORT
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2019-01-25 Released: 2020-01-29
Deposition Author(s): Wang, M., Wang, H., Sun, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.219
R-Value Work: 0.189
R-Value Observed: 0.190

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Binding of ruthenium and osmium at non-iron sites of transferrin explains their iron-independent cellular uptake

Wang, M., Wang, H., Sun, H.

To be published.

Macromolecule Content

Total Structure Weight: 75.69 kDa
Atom Count: 5,144
Modelled Residue Count: 656
Deposited Residue Count: 679
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serotransferrin	A	679	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P02787 (Homo sapiens) Explore P02787 Go to UniProtKB: P02787
PHAROS: P02787 GTEx: ENSG00000091513
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02787
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MLI Query on MLI Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.219
R-Value Work: 0.189
R-Value Observed: 0.190
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.567	α = 90
b = 157.153	β = 90
c = 107.265	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2020-01-29

Deposition Author(s):

Wang, M.

Wang, H.

Sun, H.

Revision History (Full details and data files)

Version 1.0: 2020-01-29
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description

Prepare Data

Validate Data

Deposit Data

Help and Resources

6JAS

Human serum transferrin with iron citrate bound

Binding of ruthenium and osmium at non-iron sites of transferrin explains their iron-independent cellular uptake

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)