- PDB-4c2z: Human N-myristoyltransferase (NMT1) with Myristoyl-CoA and inhibi... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4c2z
Title
Human N-myristoyltransferase (NMT1) with Myristoyl-CoA and inhibitor bound
Components
GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE 1
Keywords
TRANSFERASE / MYRISTOYLATION
Function / homology
Function and homology information
myristoyltransferase activity / peptidyl-lysine N6-myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / Late Phase of HIV Life Cycle / cellular ketone metabolic process / regulation of opsin-mediated signaling pathway / Activation, myristolyation of BID and translocation to mitochondria / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / protein localization to membrane ...myristoyltransferase activity / peptidyl-lysine N6-myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / Late Phase of HIV Life Cycle / cellular ketone metabolic process / regulation of opsin-mediated signaling pathway / Activation, myristolyation of BID and translocation to mitochondria / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / protein localization to membrane / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Inactivation, recovery and regulation of the phototransduction cascade / in utero embryonic development / plasma membrane / cytoplasm / cytosol Similarity search - Function
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9783 Å / Relative weight: 1
Reflection
Resolution: 2.08→89 Å / Num. obs: 50468 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 12.9
Reflection shell
Resolution: 2.08→2.14 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 3.4 / % possible all: 100
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0033
refinement
XDS
datareduction
SCALA
datascaling
Refinement
Method to determine structure: OTHER Starting model: NONE Resolution: 2.08→89.56 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.388 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23814
2515
5 %
RANDOM
Rwork
0.16939
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obs
0.17273
47889
99.92 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK