Structure of PDB 5vp2 Chain 1E

Receptor sequence

>5vp21E (length=204) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence]

MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLG
FLPQNPKRVNRPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGE
RVDVTGTSKGRGFAGVMKRWNFAGGPDSHGAHKIHRHPGSIGNRKTPGRV
YKGKKMAGHYGAERVTVMNLEVVDVIPEENLLLVKGAVPGPNGGLVIVRE
TKKA

3D structure

PDB

5vp2 Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state.

Chain

Resolution

2.8 Å

3D
structure

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Enzymatic activity

Enzyme Commision number

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)
BS01	rna	1E	M11 T12 R13 P22 Q35 R37 K41 D42 Y44 Q48 R58 N60 R61 P62 L63 G65 H66 K69 R76 L78 R79 E80 R82 K109 G110 R111 G112 F113 G115 M117 K118 R119 N121 F122 A123 D127 S128 H129 G130 H132 K133 I134 H135 R136 H137 P138 G139 S140 I141 G142 N143 R144 K145 T146 P147 G148 R149 V150 Y151 K152 G153 K154 M156 A157 H159 Y160 R164 V165 T166 M168 N169 K185 G186 A187 V188 P189 G190 P191 N192 K202 K203	M11 T12 R13 P22 Q35 R37 K41 D42 Y44 Q48 R58 N60 R61 P62 L63 G65 H66 K69 R76 L78 R79 E80 R82 K109 G110 R111 G112 F113 G115 M117 K118 R119 N121 F122 A123 D127 S128 H129 G130 H132 K133 I134 H135 R136 H137 P138 G139 S140 I141 G142 N143 R144 K145 T146 P147 G148 R149 V150 Y151 K152 G153 K154 M156 A157 H159 Y160 R164 V165 T166 M168 N169 K185 G186 A187 V188 P189 G190 P191 N192 K202 K203
BS02	MG	1E	V116 M117 R136	V116 M117 R136
BS03	MG	1E	K118 R119 Y160	K118 R119 Y160
BS04	MG	1E	G106 T107 G194 L195	G106 T107 G194 L195

Gene Ontology

	Molecular Function
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

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:5vp2, PDBe:5vp2, PDBj:5vp2
PDBsum	5vp2
PubMed	28505372
UniProt	Q5SHN8\|RL3_THET8 Large ribosomal subunit protein uL3 (Gene Name=rplC)

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