1VQK: CCDA-PHE-CAP-BIO

The structure of CCDA-PHE-CAP-BIO bound to the a site of the ribosomal subunit of haloarcula marismortui. Determined by X-ray diffraction at 2.3 Å resolution. Released 29 Nov 2005.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Haloarcula marismortui
Chains: 32
Atoms: 99,036
Mol. weight: 1489.96 kDa
Ligands: CD, SR, MG
Released: 29 Nov 2005

Explore 1VQK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1VQK contains 196 α-helices and 194 β-strands across 29 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 1: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	5-8	4
β-strand	16-18	3	4
β-strand	25-28	4	4
β-strand	33-34	2	4
α-helix	45-46	2
α-helix	49-51	3

Chain 2: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	5-17	13
α-helix	23-28	6

Chain 3: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	14
β-strand	6-11	6	15
β-strand	16-24	9	15
α-helix	25-30	6
α-helix	35-43	9
α-helix	50-53	4
α-helix	63	1
β-strand	64	1	16
α-helix	65	1
β-strand	67-71	5	15
β-strand	77-78	2	15
β-strand	84	1	16
β-strand	89-91	3	14

Chain A: 13 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	5-10	6
α-helix	14-16	3
α-helix	20-22	3
α-helix	28-31	4
β-strand	39-48	10	5
β-strand	53-60	8	5
β-strand	65-68	4	5
α-helix	70	1
β-strand	71	1	6
β-strand	75	1	3
β-strand	79-81	3	5
β-strand	82	1	7
β-strand	93-95	3	7
α-helix	96-98	3
α-helix	100	1
β-strand	104-106	3	7
β-strand	108	1	8
β-strand	118	1	8
β-strand	126-130	5	7
β-strand	136-139	4	7
β-strand	145-148	4	7
β-strand	153-156	4	7
α-helix	158	1
β-strand	159	1	6
α-helix	164-166	3
α-helix	172-179	8
α-helix	191-193	3
α-helix	196-198	3
β-strand	214-215	2	9
α-helix	219-220	2
β-strand	227-228	2	9

Chain B: 11 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	30-31	2
β-strand	37-38	2	10
β-strand	41-54	14	11
β-strand	66-75	10	11
β-strand	79-90	12	10
β-strand	93-101	9	10
α-helix	109-111	3
α-helix	121-134	14
β-strand	137-145	9	10
α-helix	148-150	3
α-helix	159-160	2
β-strand	161-167	7	10
α-helix	171-184	14
β-strand	187-188	2	10
β-strand	199-205	7	11
α-helix	206-207	2
β-strand	208-212	5	12
α-helix	214-218	5
α-helix	220-223	4
α-helix	225-228	4
β-strand	255-258	4	12
β-strand	261-275	15	11
α-helix	279-280	2
β-strand	284	1	13
β-strand	288	1	13
β-strand	292-298	7	11
β-strand	308-313	6	11
β-strand	327-330	4	11

Chain C: 16 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	17
β-strand	12-17	6	17
α-helix	18-19	2
α-helix	20-23	4
α-helix	25-26	2
α-helix	28-41	14
α-helix	43-45	3
β-strand	59	1	18
β-strand	72-73	2	18
β-strand	76-77	2	18
α-helix	104-117	14
α-helix	121-127	7
β-strand	138-140	3	17
α-helix	142-146	5
α-helix	150-159	10
α-helix	164-169	6
β-strand	173-174	2	19
α-helix	178-182	5
β-strand	186-187	2	19
β-strand	193-196	4	17
α-helix	202-205	4
β-strand	211-214	4	17
α-helix	220-223	4
α-helix	225-227	3
β-strand	233-236	4	17
α-helix	237-242	6
α-helix	243-245	3

Chain D: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	17-26	10	21
α-helix	38-44	7
β-strand	50-52	3	21
β-strand	58	1	22
β-strand	62	1	22
β-strand	70-75	6	21
α-helix	78-87	10
α-helix	88-90	3
β-strand	98	1	21
β-strand	104-106	3	21
β-strand	129-135	7	21
α-helix	139-142	4
α-helix	150-152	3
α-helix	159-167	9

Chain E: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	23
α-helix	7-8	2
β-strand	12-16	5	24
β-strand	19-24	6	24
β-strand	27-32	6	24
β-strand	39-43	5	23
β-strand	46-50	5	23
α-helix	56-76	21
β-strand	80-87	8	25
β-strand	94-98	5	26
β-strand	101-105	5	26
α-helix	107-109	3
α-helix	113	1
β-strand	114-117	4	26
α-helix	118-119	2
β-strand	123-127	5	25
β-strand	130-135	6	25
α-helix	138-150	13
β-strand	165-170	6	25

21 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
23S ribosomal rna	0	RNA	2922	Haloarcula marismortui
5S ribosomal RNA	9	RNA	122	Haloarcula marismortui
5'-r(cpcp(da)(phe)*(aca))-3'	4	RNA	5
50S ribosomal protein L2P	A	protein	240	Haloarcula marismortui	P20276 (AlphaFold model)
50S ribosomal protein L3P	B	protein	338	Haloarcula marismortui	P20279 (AlphaFold model)
50S ribosomal protein L4E	C	protein	246	Haloarcula marismortui	P12735 (AlphaFold model)
50S ribosomal protein L5P	D	protein	177	Haloarcula marismortui	P14124 (AlphaFold model)
50S ribosomal protein L6P	E	protein	178	Haloarcula marismortui	P14135
50S ribosomal protein L7AE	F	protein	120	Haloarcula marismortui	P12743
Acidic ribosomal protein P0 homolog	G	protein	348	Haloarcula marismortui	P15825
50S ribosomal protein L10E	H	protein	171	Haloarcula marismortui	P60617
50S ribosomal protein L13P	J	protein	145	Haloarcula marismortui	P29198

20 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>1VQK_1 23S ribosomal rna (chains 0)
UUGGCUACUAUGCCAGCUGGUGGAUUGCUCGGCUCAGGCGCUGAUGAAGGACGUGCCAAG
CUGCGAUAAGCCAUGGGGAGCCGCACGGAGGCGAAGAACCAUGGAUUUCCGAAUGAGAAU
CUCUCUAACAAUUGCUUCGCGCAAUGAGGAACCCCGAGAACUGAAACAUCUCAGUAUCGG
GAGGAACAGAAAACGCAAUGUGAUGUCGUUAGUAACCGCGAGUGAACGCGAUACAGCCCA
AACCGAAGCCCUCACGGGCAAUGUGGUGUCAGGGCUACCUCUCAUCAGCCGACCGUCUCG
ACGAAGUCUCUUGGAACAGAGCGUGAUACAGGGUGACAACCCCGUACUCGAGACCAGUAC
GACGUGCGGUAGUGCCAGAGUAGCGGGGGUUGGAUAUCCCUCGCGAAUAACGCAGGCAUC
GACUGCGAAGGCUAAACACAACCUGAGACCGAUAGUGAACAAGUAGUGUGAACGAACGCU
GCAAAGUACCCUCAGAAGGGAGGCGAAAUAGAGCAUGAAAUCAGUUGGCGAUCGAGCGAC
AGGGCAUACAAGGUCCCUCGACGAAUGACCGACGCGCGAGCGUCCAGUAAGACUCACGGG
AAGCCGAUGUUCUGUCGUACGUUUUGAAAAACGAGCCAGGGAGUGUGUCUGCAUGGCAAG
UCUAACCGGAGUAUCCGGGGAGGCACAGGGAAACCGACAUGGCCGCAGGGCUUUGCCCGA
GGGCCGCCGUCUUCAAGGGCGGGGAGCCAUGUGGACACGACCCGAAUCCGGACGAUCUAC
GCAUGGACAAGAUGAAGCGUGCCGAAAGGCACGUGGAAGUCUGUUAGAGUUGGUGUCCUA
CAAUACCCUCUCGUGAUCUAUGUGUAGGGGUGAAAGGCCCAUCGAGUCCGGCAACAGCUG
GUUCCAAUCGAAACAUGUCGAAGCAUGACCUCCGCCGAGGUAGUCUGUGAGGUAGAGCGA
CCGAUUGGUGUGUCCGCCUCCGAGAGGAGUCGGCACACCUGUCAAACUCCAAACUUACAG
ACGCCGUUUGACGCGGGGAUUCCGGUGCGCGGGGUAAGCCUGUGUACCAGGAGGGGAACA
ACCCAGAGAUAGGUUAAGGUCCCCAAGUGUGGAUUAAGUGUAAUCCUCUGAAGGUGGUCU
CGAGCCCUAGACAGCCGGGAGGUGAGCUUAGAAGCAGCUACCCUCUAAGAAAAGCGUAAC
AGCUUACCGGCCGAGGUUUGAGGCGCCCAAAAUGAUCGGGACUCAAAUCCACCACCGAGA
CCUGUCCGUACCACUCAUACUGGUAAUCGAGUAGAUUGGCGCUCUAAUUGGAUGGAAGUA
GGGGUGAAAACUCCUAUGGACCGAUUAGUGACGAAAAUCCUGGCCAUAGUAGCAGCGAUA
GUCGGGUGAGAACCCCGACGGCCUAAUGGAUAAGGGUUCCUCAGCACUGCUGAUCAGCUG
AGGGUUAGCCGGUCCUAAGUCAUACCGCAACUCGACUAUGACGAAAUGGGAAACGGGUUA
AUAUUCCCGUGCCACUAUGCAGUGAAAGUUGACGCCCUGGGGUCGAUCACGCUGGGCAUU
CGCCCAGUCGAACCGUCCAACUCCGUGGAAGCCGUAAUGGCAGGAAGCGGACGAACGGCG
GCAUAGGGAAACGUGAUUCAACCUGGGGCCCAUGAAAAGACGAGCAUAGUGUCCGUACCG
AGAACCGACACAGGUGUCCAUGGCGGCGAAAGCCAAGGCCUGUCGGGAGCAACCAACGUU
AGGGAAUUCGGCAAGUUAGUCCCGUACCUUCGGAAGAAGGGAUGCCUGCUCCGGAACGGA
GCAGGUCGCAGUGACUCGGAAGCUCGGACUGUCUAGUAACAACAUAGGUGACCGCAAAUC
CGCAAGGACUCGUACGGUCACUGAAUCCUGCCCAGUGCAGGUAUCUGAACACCUCGUACA
AGAGGACGAAGGACCUGUCAACGGCGGGGGUAACUAUGACCCUCUUAAGGUAGCGUAGUA
CCUUGCCGCAUCAGUAGCGGCUUGCAUGAAUGGAUUAACCAGAGCUUCACUGUCCCAACG
UUGGGCCCGGUGAACUGUACAUUCCAGUGCGGAGUCUGGAGACACCCAGGGGGAAGCGAA
GACCCUAUGGAGCUUUACUGCAGGCUGUCGCUGAGACGUGGUCGCCGAUGUGCAGCAUAG
GUAGGAGACACUACACAGGUACCCGCGCUAGCGGGCCACCGAGUCAACAGUGAAAUACUA
CCCGUCGGUGACUGCGACUCUCACUCCGGGAGGAGGACACCGAUAGCCGGGCAGUUUGAC
UGGGGCGGUACGCGCUCGAAAAGAUAUCGAGCGCGCCCUAUGGCUAUCUCAGCCGGGACA
GAGACCCGGCGAAGAGUGCAAGAGCAAAAGAUAGCUUGACAGUGUUCUUCCCAACGAGGA
ACGCUGACGCGAAAGCGUGGUCUAGCGAACCAAUUAGCCUGCUUGAUGCGGGCAAUUGAU
GACAGAAAAGCUACCCUAGGGAUAACAGAGUCGUCACUCGCAAGAGCACAUAUCGACCGA
GUGGCUUGCUACCUCGAUGUCGGUUCCCUCCAUCCUGCCCGUGCAGAAGCGGGCAAGGGU
GAGGUUGUUCGCCUAUUAAAGGAGGUCGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUC
GGCUGCUAUCUACUGGGUGUGUAAUGGUGUCUGACAAGAACGACCGUAUAGUACGAGAGG
AACUACGGUUGGUGGCCACUGGUGUACCGGUUGUUCGAGAGAGCACGUGCCGGGUAGCCA
CGCCACACGGGGUAAGAGCUGAACGCAUCUAAGCUCGAAACCCACUUGGAAAAGAGACAC
CGCCGAGGUCCCGCGUACAAGACGCGGUCGAUAGACUCGGGGUGUGCGCGUCGAGGUAAC
GAGACGUUAAGCCCACGAGCACUAACAGACCAAAGCCAUCAU

Sequence of entity 2 (9), FASTA

>1VQK_2 5S ribosomal RNA (chains 9)
UUAGGCGGCCACAGCGGUGGGGUUGCCUCCCGUACCCAUCCCGAACACGGAAGAUAAGCC
CACCAGCGUUCCGGGGAGUACUGGAGUGCGCGAGCCUCUGGGAAACCCGGUUCGCCGCCA
CC

Sequence of entity 3 (4), FASTA

>1VQK_3 5'-R(*CP*CP*(DA)*(PHE)*(ACA))-3' (chains 4)
CCAFX

Sequence of entity 4 (A), FASTA

>1VQK_4 50S ribosomal protein L2P (chains A)
MGRRIQGQRRGRGTSTFRAPSHRYKADLEHRKVEDGDVIAGTVVDIEHDPARSAPVAAVE
FEDGDRRLILAPEGVGVGDELQVGVSAEIAPGNTLPLAEIPEGVPVCNVESSPGDGGKFA
RASGVNAQLLTHDRNVAVVKLPSGEMKRLDPQCRATIGVVAGGGRTDKPFVKAGNKHHKM
KARGTKWPNVRGVAMNAVDHPFGGGGRQHPGKPKSISRNAPPGRKVGDIASKRTGRGGNE

Sequence of entity 5 (B), FASTA

>1VQK_5 50S ribosomal protein L3P (chains B)
MPQPSRPRKGSLGFGPRKRSTSETPRFNSWPSDDGQPGVQGFAGYKAGMTHVVLVNDEPN
SPREGMEETVPVTVIETPPMRAVALRAYEDTPYGQRPLTEVWTDEFHSELDRTLDVPEDH
DPDAAEEQIRDAHEAGDLGDLRLITHTVPDAVPSVPKKKPDVMETRVGGGSVSDRLDHAL
DIVEDGGEHAMNDIFRAGEYADVAGVTKGKGTQGPVKRWGVQKRKGKHARQGWRRRIGNL
GPWNPSRVRSTVPQQGQTGYHQRTELNKRLIDIGEGDEPTVDGGFVNYGEVDGPYTLVKG
SVPGPDKRLVRFRPAVRPNDQPRLDPEVRYVSNESNQG

Sequence of entity 6 (C), FASTA

>1VQK_6 50S ribosomal protein L4E (chains C)
MQATIYDLDGNTDGEVDLPDVFETPVRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPAES
FGSGRGQAHVPKLDGRARRVPQAVKGRSAHPPKTEKDRSLDLNDKERQLAVRSALAATAD
ADLVADRGHEFDRDEVPVVVSDDFEDLVKTQEVVSLLEALDVHADIDRADETKIKAGQGS
ARGRKYRRPASILFVTSDEPSTAARNLAGADVATASEVNTEDLAPGGAPGRLTVFTESAL
AEVAER

Sequence of entity 7 (D), FASTA

>1VQK_7 50S ribosomal protein L5P (chains D)
MSSESESGGDFHEMREPRIEKVVVHMGIGHGGRDLANAEDILGEITGQMPVRTKAKRTVG
EFDIREGDPIGAKVTLRDEMAEEFLQTALPLAELATSQFDDTGNFSFGVEEHTEFPSQEY
DPSIGIYGLDVTVNLVRPGYRVAKRDKASRSIPTKHRLNPADAVAFIESTYDVEVSE

Sequence of entity 8 (E), FASTA

>1VQK_8 50S ribosomal protein L6P (chains E)
MPRVELEIPEDVDAEQDHLDITVEGDNGSVTRRLWYPDIDVSVDGDTVVIESDEDNAKTM
STIGTFQSHIENMFHGVTEGWEYGMEVFYSHFPMQVNVEGDEVVIENFLGEKAPRRTTIH
GDTDVEIDGEELTVSGPDIEAVGQTAADIEQLTRINDKDVRVFQDGVYITRKPNRGDA

Sequence of entity 9 (F), FASTA

>1VQK_9 50S ribosomal protein L7AE (chains F)
MPVYVDFDVPADLEDDALEALEVARDTGAVKKGTNETTKSIERGSAELVFVAEDVQPEEI
VMHIPELADEKGVPFIFVEQQDDLGHAAGLEVGSAAAAVTDAGEADADVEDIADKVEELR

Sequence of entity 10 (G), FASTA

>1VQK_10 ACIDIC RIBOSOMAL PROTEIN P0 HOMOLOG (chains G)
MSAESERKTETIPEWKQEEVDAIVEMIESYESVGVVNIAGIPSRQLQDMRRDLHGTAELR
VSRNTLLERALDDVDDGLEDLNGYITGQVGLIGTDDNPFSLFQELEASKTPAPIGAGEVA
PNDIVIPEGDTGVDPGPFVGELQSVGADARIQEGSIQVLSDSTVLDTGEEVSQELSNVLN
ELGIEPKEVGLDLRAVFADGVLFEPEELELDIDEYRSDIQAAAGRAFNLSVNADYPTATT
APTMLQSDRGNAKSLALQAAIEDPEVVPDLVSKADAQVRALASQIDDEEALPEELQGVEA
DVATEEPTDDQDDDTASEDDADADDAAEEADDDDDDDEDAGDALGAMF

Sequence of entity 11 (H), FASTA

>1VQK_11 50S RIBOSOMAL PROTEIN L10E (chains H)
KPASMYRDIDKPAYTRREYITGIPGSKIAQHKMGRKQKDADDYPVQISLIVEETVQLRHG
SLEASRLSANRHLIKELGEEGDYKMTLRKFPHQVLRENKQATGAGADRVSDGMRAAFGKI
VGTAARVQAGEQLFTAYCNVEDAEHVKEAFRRAYNKITPSCRIDSSPAGNA

Sequence of entity 12 (J), FASTA

>1VQK_12 50S ribosomal protein L13P (chains J)
MSVAEFDADVIVDARDCIMGRVASQVAEQALDGETVAVVNAERAVITGREEQIVEKYEKR
VDIGNDNGYFYPKRPDGIFKRTIRGMLPHKKQRGREAFESVRVYLGNPYDEDGEVLDGTS
LDRLSNIKFVTLGEISETLGANKTW

Ligands and cofactors

ID	Name	Formula	Copies
CD	Cadmium ion	Cd	5
SR	Strontium ion	Sr	114
MG	Magnesium ion	Mg	93

Water and common crystallization additives (CL, NA, K) are not listed.

Primary citation

Structural Insights into the Roles of Water and the 2' Hydroxyl of the P Site tRNA in the Peptidyl Transferase Reaction. Schmeing, T.M., Huang, K.S., Kitchen, D.E. et al. Mol Cell (2005) 20:437-448. DOI 10.1016/j.molcel.2005.09.006 · PubMed

Other PDB entries of the same protein (UniProt P20276 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1VQ8 2.2 Å, The structure of CCDA-PHE-CAP-BIO and the antibiotic sparsomycin bound to the large…
1VQO 2.2 Å, The structure of CCPMN bound to the large ribosomal subunit haloarcula marismortui
1VQP 2.25 Å, The structure of the transition state analogue "RAP" bound to the large ribosomal…
1VQL 2.3 Å, The structure of the transition state analogue "DCSN" bound to the large ribosomal…
1VQM 2.3 Å, The structure of the transition state analogue "DAN" bound to the large ribosomal…
1FFK 2.4 Å, Crystal structure of the large ribosomal subunit from haloarcula marismortui at 2.4 Å…
1JJ2 2.4 Å, Fully Refined Crystal Structure of the Haloarcula marismortui Large Ribosomal Subunit at…
1S72 2.4 Å, Refined crystal structure of the haloarcula marismortui large ribosomal subunit at 2.4 Å…
1VQ9 2.4 Å, The structure of CCA-PHE-CAP-BIO and the antibiotic sparsomycin bound to the large…
1VQN 2.4 Å, The structure of CC-HPMN AND CCA-PHE-CAP-BIO bound to the large ribosomal subunit of…
1YHQ 2.4 Å, Crystal Structure Of Azithromycin Bound To The G2099A Mutant 50S Ribosomal Subunit Of…
3CC2 2.4 Å, The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at…

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