7JVS | pdb_00007jvs

Crystal Structure of an Essential Ribosomal Processing Protease Prp from S. aureus in complex with a Substrate Peptide

PDB DOI: https://doi.org/10.2210/pdb7JVS/pdb

Classification: HYDROLASE
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2020-08-22 Released: 2021-09-01
Deposition Author(s): Wright, H.T., Peterson, D.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.264 (Depositor), 0.264 (DCC)
R-Value Work:
0.224 (Depositor), 0.226 (DCC)
R-Value Observed:
0.227 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of an Essential Ribosomal Processing Protease Prp from S. aureus in complex with a Substrate Peptide

Wright, H.T., Peterson, D., Christie, G.

To be published.

Macromolecule Content

Total Structure Weight: 24.95 kDa
Atom Count: 1,691
Modeled Residue Count: 223
Deposited Residue Count: 226
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal-processing cysteine protease Prp	A [auth B], C [auth D]	106	Staphylococcus aureus	Mutation(s): 2 Gene Names: BN1321_260284, BTN44_03930, C7P97_01985, CSC87_06715, DD544_01544, DD547_01729, DDL17_04735, DQV20_11645, DQV53_09155, E3A28_00240... BN1321_260284, BTN44_03930, C7P97_01985, CSC87_06715, DD544_01544, DD547_01729, DDL17_04735, DQV20_11645, DQV53_09155, E3A28_00240, E3K14_08315, E4U00_05990, EP54_09330, EQ90_02345, ERS072840_00776, FA040_12870, FVP29_06750, GF545_03610, GIX97_04380, GO677_13485, GO706_06595, GO746_11035, GO793_02925, GO793_12515, GO803_01985, GO805_05045, GO810_16085, GO821_00235, GO894_13395, GO915_03870, GO941_09805, HMPREF3211_01798, M1K003_1397, NCTC10654_01710, NCTC10702_02585, NCTC5664_03624, NCTC6133_02188, NCTC7878_03165, RK64_08805, SAMEA1029528_01686, SAMEA1029547_02076, SAMEA1029553_02519, SAMEA1469856_00607, SAMEA1469884_01223, SAMEA1531680_00288, SAMEA1531701_01205, SAMEA1964876_02447, SAMEA1965205_02481, SAMEA1966505_02490, SAMEA1969349_02416, SAMEA1969845_01676, SAMEA1971706_01055, SAMEA1972827_01838, SAMEA2076212_01600, SAMEA2076218_01666, SAMEA2076220_01752, SAMEA2076226_01556, SAMEA2076463_02381, SAMEA2076464_02394, SAMEA2076470_02431, SAMEA2076472_02346, SAMEA2076478_02402, SAMEA2076480_02456, SAMEA2076481_02468, SAMEA2076743_02501, SAMEA2076745_02445, SAMEA2076746_02444, SAMEA2076747_02486, SAMEA2076749_02400, SAMEA2076751_02425, SAMEA2076752_02493, SAMEA2076755_02464, SAMEA2076756_02514, SAMEA2076758_02521, SAMEA2076759_02515, SAMEA2076761_02557, SAMEA2076762_01945, SAMEA2076763_01877, SAMEA2076764_02486, SAMEA2076765_02396, SAMEA2077023_02451, SAMEA2077025_02500, SAMEA2077027_02451, SAMEA2077029_02463, SAMEA2077031_02497, SAMEA2077034_01994, SAMEA2077035_02483, SAMEA2077039_02486, SAMEA2077040_02404, SAMEA2077041_02447, SAMEA2077044_02452, SAMEA2077045_02427, SAMEA2077046_02417, SAMEA2077293_02510, SAMEA2077294_02438, SAMEA2077295_02425, SAMEA2077297_02396, SAMEA2077300_02477, SAMEA2077301_02476, SAMEA2077302_02443, SAMEA2077303_02458, SAMEA2077307_02357, SAMEA2078252_02489, SAMEA2078256_02457, SAMEA2078307_02502, SAMEA2078308_02409, SAMEA2078553_02399, SAMEA2078558_02472, SAMEA2078560_02496, SAMEA2078569_00046, SAMEA2078570_02413, SAMEA2078572_02514, SAMEA2078824_02435, SAMEA2079048_02570, SAMEA2079051_02465, SAMEA2079277_01808, SAMEA2079291_02682, SAMEA2079503_02553, SAMEA2079507_01005, SAMEA2079512_02667, SAMEA2079517_02674, SAMEA2079724_01337, SAMEA2079727_01612, SAMEA2079728_01943, SAMEA2079732_01656, SAMEA2079946_01624, SAMEA2079949_01591, SAMEA2079952_01419, SAMEA2079957_01912, SAMEA2079958_01822, SAMEA2079960_01835, SAMEA2079961_01609, SAMEA2079968_01340, SAMEA2080329_01468, SAMEA2080330_01912, SAMEA2080334_01932, SAMEA2080433_01740, SAMEA2080812_02522, SAMEA2080898_02518, SAMEA2080900_02445, SAMEA2080904_02459, SAMEA2080913_02507, SAMEA2081043_02492, SAMEA2081053_02569, SAMEA2081054_02533, SAMEA2081055_02521, SAMEA2081060_01823, SAMEA2081211_00857, SAMEA2081213_00881, SAMEA2081218_01649, SAMEA2081341_01341, SAMEA2081342_01612, SAMEA2081349_01864, SAMEA2081359_01619, SAMEA2081362_01623, SAMEA2081468_02419, SAMEA2081474_02496, SAMEA2081475_02467, SAMEA2081476_02433, SAMEA2081479_02517, SAMEA2081480_02464, SAMEA2081560_02361, SAMEA2081561_02437, SAMEA2081564_02416, SAMEA2081567_02404, SAMEA2081568_02500, SAMEA2081569_02476, SAMEA2081570_02367, SAMEA2081571_02441, SAMEA2081572_02441, SAMEA2081573_02444, SAMEA2081575_02417, SAMEA2081577_02472, SAMEA2081578_02440, SAMEA2081579_02464, SAMEA2081581_02376, SAMEA2081582_02553, SAMEA2081673_01456, SAMEA2081674_01693, SAMEA958766_01141, SAMEA958770_01541, SAMEA958772_01367, SAMEA958778_01377, SAMEA958779_02720, SAMEA958785_01190, SAMEA958793_01565, SAMEA958798_01254, SAMEA958804_01429, SAMEA958810_02901, SAMEA958836_01614, SAMEA958838_02812, SAMEA958845_01498, SAMEA958846_01744, SAMEA958848_02333, SAMEA958855_02126, SAMEA958858_02293, SAMEA958870_02489, SAMEA958898_01783, SAMEA958906_02170, SAMEA958924_01277, SAMEA958925_01299, SAMEA958951_01296, SAMEA958953_00896, SAMEA958961_01996, SAMEA958979_01146, SAMEA958987_02151, SAMEA958995_01155, SAST44_01826, SAST45_01804 EC: 3.4.22
UniProt
Find proteins for Q2FXS9 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FXS9 Go to UniProtKB: Q2FXS9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2FXS9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
L27 ribosomal peptide	B [auth C]	14	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for Q2FXT0 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FXT0 Go to UniProtKB: Q2FXT0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2FXT0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain F [auth D] MOL2 format, chain F [auth D] mmCIF format, chain F [auth D]	F [auth D]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain F [auth D] Interactions & Density Focus chain F [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain E [auth D] SDF format, chain D [auth B] MOL2 format, chain E [auth D] MOL2 format, chain D [auth B] mmCIF format, chain E [auth D] mmCIF format, chain D [auth B]	D [auth B], E [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain E [auth D] Interactions & Density Focus chain D [auth B] Focus chain E [auth D]