Home Research COVID-19 Services Publications People Teaching Job Opening News Forum Lab Only

Online Services

●I-TASSER ●I-TASSER-MTD ●C-I-TASSER ●CR-I-TASSER ●QUARK ●C-QUARK ●LOMETS ●MUSTER ●CEthreader ●SEGMER ●DeepFold ●DeepFoldRNA ●FoldDesign ●COFACTOR ●COACH ●MetaGO ●TripletGO ●IonCom ●FG-MD ●ModRefiner ●REMO ●DEMO ●DEMO-EM ●SPRING ●COTH ●Threpp ●PEPPI ●BSpred ●ANGLOR ●EDock ●BSP-SLIM ●SAXSTER ●FUpred ●ThreaDom ●ThreaDomEx ●EvoDesign ●BindProf ●BindProfX ●SSIPe ●GPCR-I-TASSER ●MAGELLAN ●ResQ ●STRUM ●DAMpred

●TM-score ●TM-align ●US-align ●MM-align ●RNA-align ●NW-align ●LS-align ●EDTSurf ●MVP ●MVP-Fit ●SPICKER ●HAAD ●PSSpred ●3DRobot ●MR-REX ●I-TASSER-MR ●SVMSEQ ●NeBcon ●ResPRE ●TripletRes ●DeepPotential ●WDL-RF ●ATPbind ●DockRMSD ●DeepMSA ●FASPR ●EM-Refiner ●GPU-I-TASSER

●BioLiP ●E. coli ●GLASS ●GPCR-HGmod ●GPCR-RD ●GPCR-EXP ●Tara-3D ●TM-fold ●DECOYS ●POTENTIAL ●RW/RWplus ●EvoEF ●HPSF ●THE-DB ●ADDRESS ●Alpaca-Antibody ●CASP7 ●CASP8 ●CASP9 ●CASP10 ●CASP11 ●CASP12 ●CASP13 ●CASP14

Structure of PDB 1w2b Chain B

Receptor sequence

>1w2bB (length=337) Species: 2238 (Haloarcula marismortui)

PQPSRPRKGSLGFGPRKRSTSETPRFNSWPSDDGQPGVQGFAGYKAGMTH
VVLVNDEPNSPREGMEETVPVTVIETPPMRAVALRAYEDTPYGQRPLTEV
WTDEFHSELDRTLDVPEDHDPDAAEEQIRDAHEAGDLGDLRLITHTVPDA
VPSVPKKKPDVMETRVGGGSVSDRLDHALDIVEDGGEHAMNDIFRAGEYA
DVAGVTKGKGTQGPVKRWGVQKRKGKHARQGWRRRIGNLGPWNPSRVRST
VPQQGQTGYHQRTELNKRLIDIGEGDEPTVDGGFVNYGEVDGPYTLVKGS
VPGPDKRLVRFRPAVRPNDQPRLDPEVRYVSNESNQG

3D structure

• PDB: 1w2b Trigger Factor in Complex with the Ribosome Forms a Molecular Cradle for Nascent Proteins
• Chain: B
• Resolution: 3.5 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	B	P1 Q2 P3 S4 R5 P6 K8 G9 S10 L11 G12 F13 G14 P15 R16 K17 R18 T20 R25 N27 S28 K45 M48 T49 H50 P70 R85 Y87 Q94 R95 P96 L97 E99 W101 R111 T112 L113 D114 P116 E117 H119 R141 K156 K157 K158 V161 E163 T206 K207 G208 K209 G210 T211 Q212 G213 K216 R217 V220 Q221 K222 K224 G225 K226 H227 R229 Q230 W232 R233 R234 R235 I236 G237 N238 L239 G240 P241 W242 N243 P244 S245 R246 V247 R248 S249 T250 Q253 Q254 Q256 Y259 Q261 R262 T263 E264 K267 D281 G282 V285 N286 G288 S300 G303 K306 R307 R312 R316 N318 S334 N335 Q336 G337	P1 Q2 P3 S4 R5 P6 K8 G9 S10 L11 G12 F13 G14 P15 R16 K17 R18 T20 R25 N27 S28 K45 M48 T49 H50 P70 R85 Y87 Q94 R95 P96 L97 E99 W101 R111 T112 L113 D114 P116 E117 H119 R141 K156 K157 K158 V161 E163 T206 K207 G208 K209 G210 T211 Q212 G213 K216 R217 V220 Q221 K222 K224 G225 K226 H227 R229 Q230 W232 R233 R234 R235 I236 G237 N238 L239 G240 P241 W242 N243 P244 S245 R246 V247 R248 S249 T250 Q253 Q254 Q256 Y259 Q261 R262 T263 E264 K267 D281 G282 V285 N286 G288 S300 G303 K306 R307 R312 R316 N318 S334 N335 Q336 G337	PDBbind-CN: Kd=1.2uM

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:1w2b, PDBe:1w2b, PDBj:1w2b
• PDBsum: 1w2b
• PubMed: 15334087
• UniProt: P20279|RL3_HALMA Large ribosomal subunit protein uL3 (Gene Name=rpl3)

zhanglabzhanggroup.org | +65-6601-1241 | Computing 1, 13 Computing Drive, Singapore 117417