3MN8

Structure of Drosophila melanogaster carboxypeptidase D isoform 1B short

PDB DOI: https://doi.org/10.2210/pdb3MN8/pdb

Classification: HYDROLASE
Organism(s): Drosophila melanogaster
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2010-04-21 Released: 2010-07-28
Deposition Author(s): Tanco, S., Arolas, J.L., Guevara, T., Lorenzo, J., Aviles, F.X., Gomis-Ruth, F.X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.282
R-Value Work: 0.211
R-Value Observed: 0.212

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 196.9 kDa
Atom Count: 12,468
Modelled Residue Count: 1,539
Deposited Residue Count: 1,740
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LP15968p	A, B, C, D	435	Drosophila melanogaster	Mutation(s): 0 Gene Names: svr-RF
UniProt
Find proteins for P42787 (Drosophila melanogaster) Explore P42787 Go to UniProtKB: P42787
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P42787
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GEM Query on GEM Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D]	G [auth A], M [auth B], P [auth C], T [auth D]	(2-GUANIDINOETHYLMERCAPTO)SUCCINIC ACID C₇ H₁₃ N₃ O₄ S VKVCLXDFOQQABP-BYPYZUCNSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain G [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain T [auth D]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain R [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D]	E [auth A], K [auth B], N [auth C], R [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain R [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain Q [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain Q [auth C]	H [auth A], I [auth A], J [auth A], Q [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain Q [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain Q [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain S [auth D] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D]	F [auth A], L [auth B], O [auth C], S [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain S [auth D] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain S [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
GEM	PDBBind: 3MN8	Ki: 670 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.282
R-Value Work: 0.211
R-Value Observed: 0.212
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.02	α = 90
b = 135.7	β = 90
c = 141.71	γ = 90

Software Package:

Software Name	Purpose
ProDC	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-07-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-07-28
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.4: 2023-09-06
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

3MN8

Structure of Drosophila melanogaster carboxypeptidase D isoform 1B short

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)