[English] 日本語
Yorodumi
- PDB-24ib: Crystal structure of human RIPK1 kinase domain in complex with co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 24ib
TitleCrystal structure of human RIPK1 kinase domain in complex with compound HR10
ComponentsReceptor-interacting serine/threonine-protein kinase 1
KeywordsTRANSFERASE / INHIBITOR
Function / homology
Function and homology information


ripoptosome assembly / positive regulation of miRNA processing / positive regulation of interleukin-6-mediated signaling pathway / death domain binding / ripoptosome assembly involved in necroptotic process / peptidyl-serine autophosphorylation / Defective RIPK1-mediated regulated necrosis / Microbial modulation of RIPK1-mediated regulated necrosis / ripoptosome / TRIF-mediated programmed cell death ...ripoptosome assembly / positive regulation of miRNA processing / positive regulation of interleukin-6-mediated signaling pathway / death domain binding / ripoptosome assembly involved in necroptotic process / peptidyl-serine autophosphorylation / Defective RIPK1-mediated regulated necrosis / Microbial modulation of RIPK1-mediated regulated necrosis / ripoptosome / TRIF-mediated programmed cell death / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TLR3-mediated TICAM1-dependent programmed cell death / TNF signaling / programmed necrotic cell death / Caspase activation via Death Receptors in the presence of ligand / SARS-CoV-1-mediated effects on programmed cell death / T cell apoptotic process / positive regulation of macrophage differentiation / JUN kinase kinase kinase activity / necroptotic signaling pathway / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / RIP-mediated NFkB activation via ZBP1 / death-inducing signaling complex / positive regulation of necroptotic process / negative regulation of necroptotic process / positive regulation of tumor necrosis factor-mediated signaling pathway / death receptor binding / positive regulation of programmed cell death / positive regulation of programmed necrotic cell death / TNFR1-induced proapoptotic signaling / positive regulation of extrinsic apoptotic signaling pathway / RIPK1-mediated regulated necrosis / TRP channels / necroptotic process / response to tumor necrosis factor / positive regulation of execution phase of apoptosis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway / canonical NF-kappaB signal transduction / signaling adaptor activity / TICAM1, RIP1-mediated IKK complex recruitment / tumor necrosis factor-mediated signaling pathway / : / protein serine/threonine kinase binding / IKK complex recruitment mediated by RIP1 / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of interleukin-8 production / TNFR1-induced NF-kappa-B signaling pathway / protein catabolic process / negative regulation of canonical NF-kappaB signal transduction / Regulation of TNFR1 signaling / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of protein phosphorylation / positive regulation of JNK cascade / Regulation of necroptotic cell death / cellular response to growth factor stimulus / cellular response to tumor necrosis factor / positive regulation of reactive oxygen species metabolic process / cellular response to hydrogen peroxide / positive regulation of tumor necrosis factor production / positive regulation of inflammatory response / Ovarian tumor domain proteases / protein autophosphorylation / positive regulation of neuron apoptotic process / response to oxidative stress / amyloid fibril formation / Potential therapeutics for SARS / positive regulation of canonical NF-kappaB signal transduction / protein kinase activity / non-specific serine/threonine protein kinase / signaling receptor complex / endosome membrane / Ub-specific processing proteases / intracellular signal transduction / positive regulation of apoptotic process / inflammatory response / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / ubiquitin protein ligase binding / positive regulation of gene expression / negative regulation of apoptotic process / protein-containing complex binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / ATP binding / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
RIP1, Death domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / : / Death-like domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site ...RIP1, Death domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / : / Death-like domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / Receptor-interacting serine/threonine-protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsTang, M.L. / Yan, H.R. / Ma, Y.Z. / Sun, N.N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal structure of human RIPK1 kinase domain in complex with compound HR10
Authors: Tang, M.L. / Yan, H.R. / Ma, Y.Z. / Sun, N.N.
History
DepositionMar 4, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Receptor-interacting serine/threonine-protein kinase 1
B: Receptor-interacting serine/threonine-protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8084
Polymers66,9372
Non-polymers8712
Water1,67593
1
A: Receptor-interacting serine/threonine-protein kinase 1
hetero molecules

B: Receptor-interacting serine/threonine-protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8084
Polymers66,9372
Non-polymers8712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_354-x-3/2,-y,z-1/21
Buried area1220 Å2
ΔGint-9 kcal/mol
Surface area23450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.504, 101.635, 130.137
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Receptor-interacting serine/threonine-protein kinase 1 / Cell death protein RIP / Receptor-interacting protein 1 / RIP-1


Mass: 33468.730 Da / Num. of mol.: 2 / Mutation: C34A, C127A, C233A, C240A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RIPK1, RIP, RIP1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q13546, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-A1E6Q / methyl (3~{S})-5-methyl-4-oxidanylidene-3-[[3-(phenylmethyl)-1~{H}-1,2,4-triazol-5-yl]carbonylamino]-2,3-dihydro-1,5-benzoxazepine-7-carboxylate


Mass: 435.433 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H21N5O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.25 M ammonium iodide, 0.03 M Gly-Gly-Glycine, 15-25% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 4, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.05→80.1 Å / Num. obs: 36440 / % possible obs: 100 % / Redundancy: 11.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.053 / Rrim(I) all: 0.182 / Χ2: 0.88 / Net I/σ(I): 10.5 / Num. measured all: 427809
Reflection shellResolution: 2.05→2.16 Å / % possible obs: 100 % / Redundancy: 9.4 % / Rmerge(I) obs: 2.444 / Num. measured all: 49087 / Num. unique obs: 5239 / CC1/2: 0.508 / Rpim(I) all: 0.845 / Rrim(I) all: 2.589 / Χ2: 0.79 / Net I/σ(I) obs: 1.4

-
Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→14.66 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2845 1840 5.08 %
Rwork0.2502 --
obs0.2519 36213 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→14.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3925 0 64 93 4082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024069
X-RAY DIFFRACTIONf_angle_d0.4915498
X-RAY DIFFRACTIONf_dihedral_angle_d19.3061498
X-RAY DIFFRACTIONf_chiral_restr0.042620
X-RAY DIFFRACTIONf_plane_restr0.003693
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.35131620.30632585X-RAY DIFFRACTION99
2.1-2.170.34531550.29692565X-RAY DIFFRACTION100
2.17-2.240.32951380.29122621X-RAY DIFFRACTION100
2.24-2.310.33711350.28142584X-RAY DIFFRACTION100
2.31-2.410.31241260.28672628X-RAY DIFFRACTION100
2.41-2.520.32661170.27242663X-RAY DIFFRACTION100
2.52-2.650.30581390.27032612X-RAY DIFFRACTION100
2.65-2.810.26731470.26962629X-RAY DIFFRACTION100
2.81-3.030.30451490.27622638X-RAY DIFFRACTION100
3.03-3.330.32321370.26162654X-RAY DIFFRACTION100
3.33-3.80.27171230.23582689X-RAY DIFFRACTION100
3.8-4.770.23571570.20922685X-RAY DIFFRACTION100
4.77-14.660.2661550.23172820X-RAY DIFFRACTION100

+
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