1TFM | pdb_00001tfm

CRYSTAL STRUCTURE OF A RIBOSOME INACTIVATING PROTEIN IN ITS NATURALLY INHIBITED FORM

PDB DOI: https://doi.org/10.2210/pdb1TFM/pdb

Classification: TOXIN
Organism(s): Viscum album
Mutation(s): No

Deposited: 2004-05-27 Released: 2004-07-13
Deposition Author(s): Mishra, V., Bilgrami, S., Paramasivam, M., Yadav, S., Sharma, R.S., Kaur, P., Srinivasan, A., Babu, C.R., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.289 (Depositor)
R-Value Work:
0.234 (Depositor)
R-Value Observed:
0.240 (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

CRYSTAL STRUCTURE OF A RIBOSOME INACTIVATING PROTEIN IN ITS NATURALLY INHIBITED FORM

Mishra, V., Bilgrami, S., Paramasivam, M., Yadav, S., Sharma, R.S., Kaur, P., Srinivasan, A., Babu, C.R., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 56.94 kDa
Atom Count: 4,101
Modeled Residue Count: 495
Deposited Residue Count: 495
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Himalayan mistletoe ribosome-inactivating protein	A	240	Viscum album	Mutation(s): 0
UniProt
Find proteins for Q6ITZ3 (Viscum album) Explore Q6ITZ3 Go to UniProtKB: Q6ITZ3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6ITZ3
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Himalayan mistletoe ribosome-inactivating protein	B	255	Viscum album	Mutation(s): 0
UniProt
Find proteins for Q6ITZ3 (Viscum album) Explore Q6ITZ3 Go to UniProtKB: Q6ITZ3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6ITZ3
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	4		N-Glycosylation	Interactions Focus chain D
Glycosylation Resources
GlyTouCan: G31886NL GlyCosmos: G31886NL GlyGen: G31886NL

Entity ID: 5
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	E	3		N-Glycosylation	Interactions Focus chain E
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	F	2		N/A	Interactions Focus chain F
Glycosylation Resources
GlyTouCan: G84224TW GlyCosmos: G84224TW GlyGen: G84224TW

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6C Query on P6C Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	2-AMINO-4-ISOPROPYL-PTERIDINE-6-CARBOXYLIC ACID C₁₀ H₁₁ N₅ O₂ GPHPGFBRJYCUDO-UHFFFAOYSA-N		Interactions Focus chain H [auth A]
NAG Query on NAG 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]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A]
GAL Query on GAL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	beta-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-FPRJBGLDSA-N		Interactions Focus chain I [auth B]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 6
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900004 Query on PRD_900004	F	beta-lactose	Oligosaccharide / Nutrient		Interactions Focus chain F

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.289 (Depositor)
R-Value Work: 0.234 (Depositor)
R-Value Observed: 0.240 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.422	α = 90
b = 109.422	β = 90
c = 309.798	γ = 120

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-07-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-07-13
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, Structure summary
Version 2.1: 2023-08-23
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-30
Changes: Structure summary