6NMM

Ternary complex structure of the T130K mutant of ANT-4 with Neomycin, AMPCPP and Pyrophosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

'Catch and Release": a Variation of the Archetypal Nucleotidyl Transfer Reaction

Selvaraj, B.Kocaman, S.Trifas, M.Serpersu, E.H.Cuneo, M.J.

(2020) ACS Catal 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kanamycin nucleotidyltransferase
A, B, C, D
256Geobacillus stearothermophilusMutation(s): 0 
UniProt
Find proteins for Q57514 (Geobacillus stearothermophilus)
Explore Q57514 
Go to UniProtKB:  Q57514
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57514
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NMY
Query on NMY

Download Ideal Coordinates CCD File 
E [auth A]
J [auth A]
L [auth B]
Q [auth C]
V [auth C]
E [auth A],
J [auth A],
L [auth B],
Q [auth C],
V [auth C],
X [auth D]
NEOMYCIN
C23 H46 N6 O13
PGBHMTALBVVCIT-VCIWKGPPSA-N
AMP
Query on AMP

Download Ideal Coordinates CCD File 
F [auth A]
K [auth A]
M [auth B]
R [auth C]
W [auth C]
F [auth A],
K [auth A],
M [auth B],
R [auth C],
W [auth C],
Y [auth D]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
PPV
Query on PPV

Download Ideal Coordinates CCD File 
G [auth A],
N [auth B],
S [auth C],
Z [auth D]
PYROPHOSPHATE
H4 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
H [auth A]
I [auth A]
O [auth B]
AA [auth D],
BA [auth D],
H [auth A],
I [auth A],
O [auth B],
P [auth B],
T [auth C],
U [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.51α = 90
b = 59.25β = 94.8
c = 102.04γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States--
Department of Energy (DOE, United States)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2020-01-29
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Database references
  • Version 1.3: 2020-05-06
    Changes: Database references
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references, Derived calculations
  • Version 2.0: 2024-05-29
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary