5DM7: 50S ribosomal protein L1

Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A. Determined by X-ray diffraction at 3.0 Å resolution. Released 11 Nov 2015.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Deinococcus radiodurans
Chains: 30
Atoms: 89,361
Mol. weight: 1360.56 kDa
Ligands: MG, HGR
Released: 11 Nov 2015

Explore 5DM7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5DM7 contains 104 α-helices and 195 β-strands across 28 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain 0: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	18-21	4
β-strand	40-41	2	1
β-strand	71	1	2
β-strand	88	1	2
α-helix	93-95	3
α-helix	113-119	7
α-helix	128-130	3
β-strand	167-168	2	1

Chain 1: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	9-14	6	69
β-strand	21-25	5	69
β-strand	36-37	2	69
β-strand	49-50	2	69

Chain 2: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-16	8
α-helix	18-23	6
α-helix	25-35	11

Chain 3: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
β-strand	15	1	9
β-strand	23-24	2	9
α-helix	38-44	7
β-strand	48-49	2	9
α-helix	56-61	6

Chain A: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	3
β-strand	18	1	3
α-helix	31-33	3
β-strand	34-36	3	4
α-helix	37-39	3
β-strand	43	1	5
β-strand	49	1	5
β-strand	61-63	3	4
α-helix	69-71	3
β-strand	77-81	5	6
β-strand	92-97	6	6
β-strand	102-106	5	6
β-strand	116-117	2	6
β-strand	119	1	7
β-strand	130	1	7
α-helix	137	1
β-strand	141-143	3	7
β-strand	145	1	8
β-strand	155	1	8
β-strand	163-167	5	7
β-strand	172-177	6	7
β-strand	181-186	6	7
β-strand	192-193	2	7
α-helix	201-203	3
α-helix	209-213	5
α-helix	218-220	3
α-helix	266-268	3
β-strand	270	1	7

Chain B: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-16	14	10
β-strand	19-27	9	10
β-strand	31	1	11
β-strand	35	1	12
α-helix	39-42	4
β-strand	46-50	5	12
β-strand	53	1	13
α-helix	56-58	3
α-helix	61-68	8
β-strand	75	1	13
β-strand	78-82	5	12
β-strand	90	1	11
β-strand	101-107	7	10
β-strand	112-114	3	14
α-helix	116-120	5
β-strand	144	1	15
β-strand	147	1	15
β-strand	158-160	3	14
β-strand	164-176	13	10
β-strand	181-185	5	10
β-strand	194-200	7	10

Chain C: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	24-37	14
α-helix	98-112	15
β-strand	117-120	4	16
α-helix	130-140	11
β-strand	148-151	4	16
α-helix	155-161	7
β-strand	167-170	4	16
α-helix	177-181	5
β-strand	185-190	6	16
α-helix	191-194	4

Chain D: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	5-17	13
β-strand	36-38	3	17
β-strand	41	1	18
β-strand	44	1	18
α-helix	47-60	14
α-helix	64-65	2
β-strand	66-69	4	17
β-strand	84-89	6	17
α-helix	93-106	14
β-strand	117	1	19
α-helix	143-145	3
β-strand	154	1	17
α-helix	163-172	10
β-strand	177	1	19

20 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
50S ribosomal protein L1	0	protein	224	Deinococcus radiodurans	Q9RSS8 (AlphaFold model)
50S ribosomal protein L2	A	protein	274	Deinococcus radiodurans	Q9RXJ9 (AlphaFold model)
50S ribosomal protein L3	B	protein	205	Deinococcus radiodurans	Q9RXK2 (AlphaFold model)
50S ribosomal protein L4	C	protein	197	Deinococcus radiodurans	Q9RXK1 (AlphaFold model)
50S ribosomal protein L5	D	protein	177	Deinococcus radiodurans	Q9RXJ0
50S ribosomal protein L6	E	protein	171	Deinococcus radiodurans	Q9RSL3
50S ribosomal protein L11	F	protein	144	Deinococcus radiodurans	Q9RSS7
50S ribosomal protein L13	G	protein	142	Deinococcus radiodurans	Q9RXY1
50S ribosomal protein L14	H	protein	134	Deinococcus radiodurans	Q9RXJ2
50S ribosomal protein L15	I	protein	141	Deinococcus radiodurans	Q9RSK9
50S ribosomal protein L16	J	protein	136	Deinococcus radiodurans	Q9RXJ5
50S ribosomal protein L17	K	protein	113	Deinococcus radiodurans	Q9RSJ5

18 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>5DM7_1 50S ribosomal protein L1 (chains 0)
KRYRALEGKVDRNKQYSIDEAAALVKELATAKFDETVEVHFRLGIDPRKSDQNVRGTVAL
PHGTGRSVRVAVITKGENVQAAEAAGADVVGSDELIERIAGGFMDFDAVVATPDMMAQIG
QKLARLLGPRGLLPNPKSGTVGADVAGMVRGLKAGRIEFRNDKTGVVHAPIGKASFESGN
LSANYQALISALEGAKPGTAKGVFLRSAYLTTTMGPSIPLALGG

Sequence of entity 2 (A), FASTA

>5DM7_2 50S ribosomal protein L2 (chains A)
AVKKYKPYTPSRRQMTTADFSGLAKKRPEKALTEALPKTGGRNNRGRITSRFIGGGHKRL
YRIIDFKRRDKSGVNAKVAAIEYDPNRSARIALLHYADGEKRYILAPEGLTVGATVNAGP
EAEPKLGNALPLRFVPVGAVVHALELVPGKGAQLARSAGTSVQVQGKESDYVIVRLPSGE
LRRVHSECYATIGAVGNAEHKNIVLGKAGRSRWLGRKPHQRGSAMNPVDHPHGGGEGRTG
AGRVPVTPWGKPTKGLKTRRKRKTSDRFLVTRRK

Sequence of entity 3 (B), FASTA

>5DM7_3 50S ribosomal protein L3 (chains B)
MKGILGTKIGMTQIWKNDRAIPVTVVLAGPCPIVQRKTAQTDGYEAVQIGYAPKAERKVN
KPMQGHFAKAGVAPTRILREFRGFAPDGDSVNVDIFAEGEKIDATGTSKGKGTQGVMKRW
NFAGGPASHGSKKWHRRPGSIGQRKTPGRVYKGKRMAGHMGMERVTVQNLEVVEIRAGEN
LILVKGAIPGANGGLVVLRSAAKAS

Sequence of entity 4 (C), FASTA

>5DM7_4 50S ribosomal protein L4 (chains C)
AQINVIGQNGGRTIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYGQ
KGTGNARHGDRSVPTFVGGGVAFGPKPRSYDYTLPRQVRQLGLAMAIASRQEGGKLVAVD
GFDIADAKTKNFISWAKQNGLDGTEKVLLVTDDENTRRAARNVSWVSVLPVAGVNVYDIL
RHDRLVIDAAALEIVEE

Sequence of entity 5 (D), FASTA

>5DM7_5 50S ribosomal protein L5 (chains D)
QLKTKYNDQVRPALMQQFGYSSVMAVPRIEKIVVNEGLGSSKEDSKAIDKAAKELALITL
QKPIITKAKKSISNFKLRQGMPVGIKVTLRGERMYVFLEKLINIGLPRIRDFRGINPNAF
DGRGNYNLGIKEQLIFPEITYDMVDKTRGMDITIVTTAKTDEEARALLQSMGLPFRK

Sequence of entity 6 (E), FASTA

>5DM7_6 50S ribosomal protein L6 (chains E)
GKQPIAVPSGVTVNAQDGVFKVKGPKGELTVPYNTELTVRQDGDQLLVERPSDAQKHRAL
HGLTRTLVANAVKGVSDGYTINLELRGVGFRAKLTGKALEMNIGYSHPVIIEPPAGVTFA
VPEPTRIDVSGIDKQLVGQVAANVRKVRKPDAYHGKGVRFVGEQIALKAGK

Sequence of entity 7 (F), FASTA

>5DM7_7 50S ribosomal protein L11 (chains F)
MRRVAGIVKLQLPAGKATPAPPVGPALGQYGANIMEFTKAFNAQTADKGDAIIPVEITIY
ADRSFTFITKTPPMSYLIRKAAGIGKGSSTPNKAKVGKLNWDQVLEIAKTKMPDLNAGSV
EAAANTVAGTARSMGVTVEGGPNA

Sequence of entity 8 (G), FASTA

>5DM7_8 50S ribosomal protein L13 (chains G)
KTYIPKNDEQNWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVINAAQVA
LTGKKLDDKVYTRYTGYQGGLKTETAREALSKHPERVIEHAVFGMLPKGRQGRAMHTRLK
VYAGETHPHSAQKPQVLKTQPL

Sequence of entity 9 (H), FASTA

>5DM7_9 50S ribosomal protein L14 (chains H)
MIMPQSRLDVADNSGAREIMCIRVLNSGIGGKGLTTGGGGNKRYAHVGDIIVASVKDAAP
RGAVKAGDVVKAVVVRTSHAIKRADGSTIRFDRNAAVIINNQGEPRGTRVFGPVARELRD
RRFMKIVSLAPEVL

Sequence of entity 10 (I), FASTA

>5DM7_10 50S ribosomal protein L15 (chains I)
HDLKPTPGSRKDRKRVGRGPGGTDKTAGRGHKGQKSRSGAGKGAFFEGGRSRLIARLPKR
GFNNVGTTYEVVKLSQLQDLEDTTFDRDTLEAYRLVRRKNRPVKLLASGEISRAVTVHVD
AASAAAIKAVEAAGGRVVLPE

Sequence of entity 11 (J), FASTA

>5DM7_11 50S ribosomal protein L16 (chains J)
KRTKFRKQFRGRMTGDAKGGDYVAFGDYGLIAMEPAWIKSNQIEACRIVMSRHFRRGGKI
YIRIFPDKPVTKKPAETRMGKGKGAVEYWVSVVKPGRVMFEVAGVTEEQAKEAFRLAGHK
LPIQTKMVKREVYDEA

Sequence of entity 12 (K), FASTA

>5DM7_12 50S ribosomal protein L17 (chains K)
HGKAGRKLNRNSSARVALARAQATALLREGRIQTTLTKAKELRPFVEQLITTAKGGDLHS
RRLVAQDIHDKDVVRKVMDEVAPKYAERPGGYTRILRVGTRRGDGVTMALIEL

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	186
HGR	Hygromycin A	C23 H29 N O12	1

Primary citation

Crystallographic characterization of the ribosomal binding site and molecular mechanism of action of Hygromycin A. Kaminishi, T., Schedlbauer, A., Fabbretti, A. et al. Nucleic Acids Res (2015) 43:10015-10025. DOI 10.1093/nar/gkv975 · PubMed

Other PDB entries of the same protein (UniProt Q9RSS8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5DM6 2.9 Å, Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans

Browse structure collections

About this viewer

MolViewer shows 5DM7 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.