5HMV

Re refinement of 4mwk.

PDB DOI: https://doi.org/10.2210/pdb5HMV/pdb
Entry: 5HMV supersedes: 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

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.6 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

PubMed: 27226979 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1063/1.4948613
Primary Citation of Related Structures:
5HMV, 5HQ1, 5I5Q, 5IDD

Organizational Affiliation

School of Chemistry, University of Manchester , Manchester M13 9PL, United Kingdom.

Macromolecule Content

Total Structure Weight: 16.32 kDa
Atom Count: 1,220
Modelled Residue Count: 128
Deposited Residue Count: 128
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	128	Gallus gallus	Mutation(s): 0 EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698 Go to UniProtKB: P00698
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00698
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PT Query on PT Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain S [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain S [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain S [auth A]	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		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain S [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain S [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain N [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain N [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain N [auth A]	B [auth A], C [auth A], N [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain N [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain N [auth A]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A]	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		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain T [auth A] MOL2 format, chain R [auth A] MOL2 format, chain T [auth A] mmCIF format, chain R [auth A] mmCIF format, chain T [auth A]	R [auth A], T [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain R [auth A] Focus chain T [auth A] Interactions & Density Focus chain R [auth A] Focus chain T [auth A]

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 = 26.998	α = 89.08
b = 31.807	β = 72
c = 34.072	γ = 67.81

Software Package:

Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
SAINT	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2016-05-18

Deposition Author(s):

Helliwell, J.R.

This entry supersedes: 4MWK

Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United 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
Version 1.6: 2024-10-16
Changes: Structure summary