2DYX | pdb_00002dyx

Structure of the complex of lactoferrin C-lobe with melibiose at 2.0 A resolution

PDB DOI: https://doi.org/10.2210/pdb2DYX/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Bos taurus
Mutation(s): No

Deposited: 2006-09-19 Released: 2006-10-03
Deposition Author(s): Mir, R., Prem kumar, R., Sinha, M., Singh, N., Sharma, S., Kaur, P., Bhushan, A., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.201 (Depositor)
R-Value Work:
0.172 (Depositor)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Structure of the complex of lactoferrin C-lobe with melibiose at 2.0 A resolution

Mir, R., Prem kumar, R., Sinha, M., Singh, N., Sharma, S., Kaur, P., Bhushan, A., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 40.75 kDa
Atom Count: 3,113
Modeled Residue Count: 341
Deposited Residue Count: 345
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactotransferrin	A	345	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
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-4)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	5		N-Glycosylation	Interactions Focus chain B
Glycosylation Resources
GlyTouCan: G60760VF GlyCosmos: G60760VF GlyGen: G60760VF

Entity ID: 3
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	2		N-Glycosylation	Interactions Focus chain C
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-beta-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	D	6		N-Glycosylation	Interactions Focus chain D
Glycosylation Resources
GlyTouCan: G38475OD GlyCosmos: G38475OD GlyGen: G38475OD

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-6)-beta-D-glucopyranose	E	2		N/A	Interactions Focus chain E
Glycosylation Resources
GlyTouCan: G87251UV GlyCosmos: G87251UV GlyGen: G87251UV

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A]
CO3 Query on CO3 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CARBONATE ION C O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-L		Interactions Focus chain G [auth A]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain F [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900041 Query on PRD_900041	E	beta-allolactose	Oligosaccharide / Inducer		Interactions Focus chain E

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.201 (Depositor)
R-Value Work: 0.172 (Depositor)
R-Value Observed: 0.173 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.588	α = 90
b = 50.4	β = 107.86
c = 65.93	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
AUTOMAR	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-10-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-10-03
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-10-25
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-11-20
Changes: Structure summary