7EV0 | pdb_00007ev0

Crystal structure of pepsin cleaved C-terminal half of lactoferrin at 2.7A resolution

PDB DOI: https://doi.org/10.2210/pdb7EV0/pdb

Classification: IRON-BINDINB PROTEIN
Organism(s): Bos taurus
Mutation(s): No

Deposited: 2021-05-19 Released: 2021-06-02
Deposition Author(s): Singh, J., Ahmad, M.I., Maurya, A., Sharma, P., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.314 (Depositor), 0.313 (DCC)
R-Value Work:
0.241 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of pepsin cleaved C-terminal half of lactoferrin at 2.7A resolution

Singh, J., Ahmad, M.I., Maurya, A., Sharma, P., Sharma, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 79.41 kDa
Atom Count: 5,620
Modeled Residue Count: 696
Deposited Residue Count: 696
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactotransferrin	A, B [auth P]	348	Bos taurus	Mutation(s): 0 EC: 3.4.21
UniProt
Find proteins for P24627 (Bos taurus) Explore P24627 Go to UniProtKB: P24627
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P24627
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B [auth P]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth Z], F [auth E]	2		N-Glycosylation	Interactions Focus chain C [auth Z] Focus chain F [auth E] Interactions & Density Focus chain C [auth Z] Focus chain F [auth E]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth B]	3		N-Glycosylation	Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth C], G [auth D]	4		N-Glycosylation	Interactions Focus chain E [auth C] Focus chain G [auth D] Interactions & Density Focus chain E [auth C] Focus chain G [auth D]
Glycosylation Resources
GlyTouCan: G08918EL GlyCosmos: G08918EL GlyGen: G08918EL

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
CO3 Query on CO3 Download:Ideal Coordinates CCD File SDF format, chain L [auth P] SDF format, chain I [auth A] MOL2 format, chain L [auth P] MOL2 format, chain I [auth A] mmCIF format, chain L [auth P] mmCIF format, chain I [auth A]	I [auth A], L [auth P]	CARBONATE ION C O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain L [auth P] Interactions & Density Focus chain I [auth A] Focus chain L [auth P]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain K [auth P] SDF format, chain H [auth A] MOL2 format, chain K [auth P] MOL2 format, chain H [auth A] mmCIF format, chain K [auth P] mmCIF format, chain H [auth A]	H [auth A], K [auth P]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth P] Interactions & Density Focus chain H [auth A] Focus chain K [auth P]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.314 (Depositor), 0.313 (DCC)
R-Value Work: 0.241 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.508	α = 90
b = 81.76	β = 130.322
c = 111.794	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2021-06-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-06-02
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary