[English] 日本語
Yorodumi
- PDB-10kv: Structure of hNSP4 bound to MCP4 at 2.75 A resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 10kv
TitleStructure of hNSP4 bound to MCP4 at 2.75 A resolution
Components
  • MCP4
  • Serine protease 57
KeywordsHYDROLASE / NSP4 / PROTEASE / MCP
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / protein maturation / azurophil granule lumen / heparin binding / serine-type endopeptidase activity / proteolysis / :
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsTang, W. / Ultsch, M.H. / Sudhamsu, J.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche LTD Switzerland
CitationJournal: J.Mol.Biol. / Year: 2026
Title: Novel macrocyclic peptides as potent and selective inhibitors of human neutrophil serine protease 4.
Authors: Tang, W. / Ultsch, M. / Adaligil, E. / Tombling, B. / Fleming, S. / Wei, Y. / Martinez, O.E. / Song, A. / Lello, P.D. / Sudhamsu, J. / Cunningham, C.N. / Kirchhofer, D.
History
DepositionJan 25, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Serine protease 57
E: MCP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1053
Polymers28,7382
Non-polymers3671
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-4 kcal/mol
Surface area11210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.150, 71.150, 149.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Serine protease 57 / Neutrophil serine protease 4 / NSP4 / Serine protease 1-like protein 1


Mass: 27002.900 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRSS57, PRSSL1, UNQ782/PRO1599 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q6UWY2, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide MCP4


Mass: 1735.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1M MES pH 6, 0.2M NaCl, 15% PEG MME 2000

-
Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.749→35.58 Å / Num. obs: 7962 / % possible obs: 75.08 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.4
Reflection shellResolution: 2.749→2.78 Å / Rmerge(I) obs: 1.559 / Num. unique obs: 24

-
Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→35.58 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.271 385 4.84 %
Rwork0.2496 --
obs0.2511 7962 75.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→35.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1887 0 24 4 1915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0231964
X-RAY DIFFRACTIONf_angle_d0.8132674
X-RAY DIFFRACTIONf_dihedral_angle_d15.45724
X-RAY DIFFRACTIONf_chiral_restr0.056299
X-RAY DIFFRACTIONf_plane_restr0.005345
LS refinement shellResolution: 3.15→3.96 Å
RfactorNum. reflection% reflection
Rfree0.3507 164 -
Rwork0.3173 3101 -
obs--93 %
Refinement TLS params.Method: refined / Origin x: -17.8961 Å / Origin y: 5.1604 Å / Origin z: 21.0923 Å
111213212223313233
T0.9854 Å20.0361 Å2-0.2449 Å2-0.4287 Å2-0.0327 Å2--0.6244 Å2
L4.9669 °24.1244 °22.6976 °2-8.2811 °23.6063 °2--8.1501 °2
S-0.8643 Å °0.5719 Å °0.4865 Å °-2.0895 Å °0.3909 Å °0.7215 Å °-1.1049 Å °0.2985 Å °0.2731 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more