4EFD | pdb_00004efd

Crystal Structure of an M17 aminopeptidase from Trypanosoma Brucei, Tb427tmp.02.4440

PDB DOI: https://doi.org/10.2210/pdb4EFD/pdb

Classification: HYDROLASE
Organism(s): Trypanosoma brucei brucei TREU927
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-03-29 Released: 2012-05-30
Deposition Author(s): Wernimont, A.K., Osman, K.T., Loppnau, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Hui, R., Lin, Y.H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.253 (Depositor), 0.248 (DCC)
R-Value Work:
0.227 (Depositor), 0.225 (DCC)
R-Value Observed:
0.228 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of an M17 aminopeptidase from Trypanosoma Brucei, Tb427tmp.02.4440

Wernimont, A.K., Osman, K.T., Loppnau, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Hui, R., Lin, Y.H.

To be published.

Macromolecule Content

Total Structure Weight: 335.23 kDa
Atom Count: 23,792
Modeled Residue Count: 3,093
Deposited Residue Count: 3,132
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminopeptidase	A, B, C, D, E A, B, C, D, E, F	522	Trypanosoma brucei brucei TREU927	Mutation(s): 0 Gene Names: Tb11.02.4440
UniProt
Find proteins for Q385B0 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q385B0 Go to UniProtKB: Q385B0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q385B0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain LA [auth F] SDF format, chain KA [auth F] SDF format, chain IA [auth E] SDF format, chain HA [auth E] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain EA [auth D] SDF format, chain DA [auth D] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain LA [auth F] MOL2 format, chain KA [auth F] MOL2 format, chain IA [auth E] MOL2 format, chain HA [auth E] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain DA [auth D] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain LA [auth F] mmCIF format, chain KA [auth F] mmCIF format, chain IA [auth E] mmCIF format, chain HA [auth E] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain DA [auth D]	DA [auth D] EA [auth D] G [auth A] H [auth A] HA [auth E] DA [auth D], EA [auth D], G [auth A], H [auth A], HA [auth E], IA [auth E], KA [auth F], LA [auth F], N [auth B], O [auth B], V [auth C], W [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain KA [auth F] Focus chain LA [auth F] Focus chain N [auth B] Focus chain O [auth B] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain KA [auth F] Focus chain LA [auth F] Focus chain N [auth B] Focus chain O [auth B] Focus chain V [auth C] Focus chain W [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain BA [auth C] SDF format, chain AA [auth C] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth C] J [auth A] K [auth A] L [auth A] AA [auth C], BA [auth C], J [auth A], K [auth A], L [auth A], R [auth B], S [auth B], T [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain NA [auth F] SDF format, chain MA [auth F] SDF format, chain FA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain NA [auth F] MOL2 format, chain MA [auth F] MOL2 format, chain FA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain NA [auth F] mmCIF format, chain MA [auth F] mmCIF format, chain FA [auth D]	FA [auth D] I [auth A] MA [auth F] NA [auth F] P [auth B] FA [auth D], I [auth A], MA [auth F], NA [auth F], P [auth B], Q [auth B], Y [auth C], Z [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain FA [auth D] Focus chain I [auth A] Focus chain MA [auth F] Focus chain NA [auth F] Focus chain P [auth B] Focus chain Q [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain FA [auth D] Focus chain I [auth A] Focus chain MA [auth F] Focus chain NA [auth F] Focus chain P [auth B] Focus chain Q [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain OA [auth F] MOL2 format, chain X [auth C] MOL2 format, chain OA [auth F] mmCIF format, chain X [auth C] mmCIF format, chain OA [auth F]	OA [auth F], X [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain OA [auth F] Focus chain X [auth C] Interactions & Density Focus chain OA [auth F] Focus chain X [auth C]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain PA [auth F] SDF format, chain M [auth A] SDF format, chain JA [auth E] SDF format, chain GA [auth D] SDF format, chain CA [auth C] MOL2 format, chain U [auth B] MOL2 format, chain PA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain GA [auth D] MOL2 format, chain CA [auth C] mmCIF format, chain U [auth B] mmCIF format, chain PA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain JA [auth E] mmCIF format, chain GA [auth D] mmCIF format, chain CA [auth C]	CA [auth C] GA [auth D] JA [auth E] M [auth A] PA [auth F] CA [auth C], GA [auth D], JA [auth E], M [auth A], PA [auth F], U [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain CA [auth C] Focus chain GA [auth D] Focus chain JA [auth E] Focus chain M [auth A] Focus chain PA [auth F] Focus chain U [auth B] Interactions & Density Focus chain CA [auth C] Focus chain GA [auth D] Focus chain JA [auth E] Focus chain M [auth A] Focus chain PA [auth F] Focus chain U [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.253 (Depositor), 0.248 (DCC)
R-Value Work: 0.227 (Depositor), 0.225 (DCC)
R-Value Observed: 0.228 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.916	α = 90
b = 161.74	β = 90
c = 176.315	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
BALBES	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-05-30

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2012-05-30
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations