5HMV

Re refinement of 4mwk.

  • Classification: HYDROLASE
  • Organism(s): Gallus gallus
  • Mutation(s): No 

  • Deposited: 2016-01-17 Released: 2016-05-18 
  • Deposition Author(s): Helliwell, J.R.
  • Funding Organization(s): Engineering and Physical Sciences Research Council

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.98 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.125 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 4mwk


Literature

Comment on "Structural dynamics of cisplatin binding to histidine in a protein" [Struct. Dyn. 1, 034701 (2014)].

Tanley, S.W.Helliwell, J.R.

(2016) Struct Dyn 3: 037101-037101


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme C128Gallus gallusMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PT
Query on PT

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
K [auth A]
L [auth A]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
S [auth A]
PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
N [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
NO3
Query on NO3

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
O [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
O [auth A],
P [auth A],
Q [auth A]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
R [auth A],
T [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.98 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.125 
  • Space Group: P 1
  • Diffraction Data: https://doi.org/10.15127/1.266899
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 26.998α = 89.08
b = 31.807β = 72
c = 34.072γ = 67.81
Software Package:
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SAINTdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Engineering and Physical Sciences Research CouncilUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-07-13
    Changes: Database references
  • Version 1.2: 2016-08-10
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2018-08-01
    Changes: Data collection, Database references
  • Version 1.5: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description