4KMK

Crystal structure of Ribosome Inactivating protein from Momordica balsamina at 1.65 A resolution

PDB DOI: https://doi.org/10.2210/pdb4KMK/pdb

Classification: HYDROLASE
Organism(s): Momordica balsamina
Mutation(s): No

Deposited: 2013-05-08 Released: 2013-05-22
Deposition Author(s): Yamini, S., Pandey, S., Kushwaha, G.S., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 ?
R-Value Free: 0.200
R-Value Work: 0.186
R-Value Observed: 0.187

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of Ribosome Inactivating protein from Momordica balsamina at 1.65 A resolution

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

To be published.

Macromolecule Content

Total Structure Weight: 27.5 kDa
Atom Count: 2,206
Modelled Residue Count: 246
Deposited Residue Count: 246
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
rRNA N-glycosidase	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 ?
R-Value Free: 0.200
R-Value Work: 0.186
R-Value Observed: 0.187
Space Group: H 3

Unit Cell:

Length ( ? )	Angle ( ? )
a = 130.14	α = 90
b = 130.14	β = 90
c = 40.05	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: 2013-05-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-05-22
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.3: 2024-10-30
Changes: Structure summary

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Help and Resources

4KMK

Crystal structure of Ribosome Inactivating protein from Momordica balsamina at 1.65 A resolution

Crystal structure of Ribosome Inactivating protein from Momordica balsamina at 1.65 A resolution

Entity ID: 1

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)