5YR7 | pdb_00005yr7

Human methionine aminopeptidase type 1b (F309L mutant)

• PDB DOI: https://doi.org/10.2210/pdb5YR7/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-11-08 Released: 2018-11-14 
• Deposition Author(s): Pillalamarri, V., Arya, T., Addlagatta, A.
• Funding Organization(s): Department of Science & Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 
  0.266 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Differential inhibition of Sub-Type 1 Methionine aminopeptidases by ovalicin

Pillalamarri, V., Arya, T., Addlagatta, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 37.23 kDa 
• Atom Count: 2,495 
• Modeled Residue Count: 304 
• Deposited Residue Count: 328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine aminopeptidase 1	A	328	Homo sapiens	Mutation(s): 1  Gene Names: METAP1, KIAA0094 EC: 3.4.11.18
UniProt & NIH Common Fund Data Resources
Find proteins for P53582 (Homo sapiens) Explore P53582  Go to UniProtKB:  P53582
PHAROS:  P53582 GTEx:  ENSG00000164024

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MET	G [auth A]	METHIONINE C5 H11 N O2 S FFEARJCKVFRZRR-BYPYZUCNSA-N
CO	B [auth A], C [auth A], D [auth A], E [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N
NA	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free:  0.266 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.414	α = 90
b = 77.193	β = 92.03
c = 48.22	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-11-14 
Deposition Author(s): Pillalamarri, V., Arya, T., Addlagatta, A.

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Funding Organization	Location	Grant Number
Department of Science & Technology	India	EMR/2015/000461

Revision History  

• Version 1.0: 2018-11-14
  Type: Initial release
  
• Version 1.1: 2019-06-26
  Changes: Data collection, Database references
• Version 1.2: 2019-11-20
  Changes: Derived calculations
• Version 1.3: 2020-05-27
  Changes: Database references
• Version 1.4: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description