3N3X | pdb_00003n3x

Crystal Structure of the complex formed between type I ribosome inactivating protein and hexapeptide Ser-Asp-Asp-Asp-Met-Gly at 1.7 A resolution

PDB DOI: https://doi.org/10.2210/pdb3N3X/pdb

Classification: HYDROLASE
Organism(s): Momordica balsamina, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Mutation(s): No

Deposited: 2010-05-20 Released: 2010-06-30
Deposition Author(s): Kushwaha, G.S., Vikram, G., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.222 (Depositor), 0.240 (DCC)
R-Value Work:
0.198 (Depositor), 0.210 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal Structure of the complex formed between type I ribosome inactivating protein and hexapeptide Ser-Asp-Asp-Asp-Met-Gly at 1.7 A resolution

Kushwaha, G.S., Vikram, G., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 28.31 kDa
Atom Count: 2,251
Modelled Residue Count: 252
Deposited Residue Count: 252
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome inactivating protein	A	246	Momordica balsamina	Mutation(s): 0 EC: 3.2.2.22
UniProt
Find proteins for D9J2T9 (Momordica balsamina) Explore D9J2T9 Go to UniProtKB: D9J2T9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D9J2T9
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SDDDMG peptide	B	6	N/A	Mutation(s): 0
UniProt
Find proteins for P02400 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P02400 Go to UniProtKB: P02400
Entity Groups
UniProt Group	P02400
Sequence Annotations Expand
Reference Sequence LOADING

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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 Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GUN Query on GUN Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GUANINE C₅ H₅ N₅ O UYTPUPDQBNUYGX-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.222 (Depositor), 0.240 (DCC)
R-Value Work: 0.198 (Depositor), 0.210 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.241	α = 90
b = 130.241	β = 90
c = 39.974	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-06-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-06-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-16
Changes: Structure summary