MolNFT v1 · #122572 · protein + RNA

Structure of the yeast kluyveromyces lactis small ribosomal subunit in complex with the cricket paralysis virus ires.

5IT9 · Ribosomal protein US2: “Structure of the yeast kluyveromyces lactis small ribosomal subunit in complex with the cricket paralysis…”. Electron microscopy, 2 ligands (MG, ZN), 20 pockets (best druggability 0.89). MolNFT v1 #122572 on…

PDB: 5IT9
Type: protein + RNA
Length: 6,820 residues
Chains: 35
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribosomal protein US2; Ribosomal protein ES1; Ribosomal protein US5; Ribosomal protein…
UniProt: Q6CN12, Q6CWD0, Q6CKL3, Q6CRK7, Q6CWJ2, Q6CRA3, Q6CM04, Q6CTD6, Q6CMG3, Q6CM18, Q6CVZ5, Q6CX80, Q6CLU4, Q6CJK0, P27069, Q6CKV4, Q875N2, Q6CWU3, Q6CWT9, Q6CXM0, Q6CIM1, Q6CXT6, Q6CW21, Q875M3, Q6CU44, Q6CW78, Q6CS01, Q6CNL2, P33285, Q6CPG3, Q6CUH5, P69061, Q6CNI7
Ligands: MG, ZN
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 35 distinct chains · 29% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribosomal protein US2	protein	206	32% helix, 9% strand	Q6CN12
B	Ribosomal protein ES1	protein	214	29% helix, 25% strand	Q6CWD0
C	Ribosomal protein US5	protein	217	31% helix, 25% strand	Q6CKL3
D	Ribosomal protein US3	protein	223	32% helix, 27% strand	Q6CRK7
E	Ribosomal protein ES4	protein	260	17% helix, 27% strand	Q6CWJ2
F	Ribosomal protein US7	protein	206	48% helix, 6% strand	Q6CRA3
G	Ribosomal protein ES6	protein	226	26% helix, 27% strand	Q6CM04
H	Ribosomal protein ES7	protein	184	35% helix, 22% strand	Q6CTD6
I	Ribosomal protein ES8	protein	188	26% helix, 18% strand	Q6CMG3
J	Ribosomal protein US4	protein	182	46% helix, 2% strand	Q6CM18
K	Ribosomal protein ES10	protein	96	43% helix, 15% strand	Q6CVZ5
L	Ribosomal protein US17	protein	155	3% helix, 26% strand	Q6CX80
M	Ribosomal protein ES12	protein	122	43% helix, 7% strand	Q6CLU4
N	Ribosomal protein US15	protein	150	57% helix, 0% strand	Q6CJK0
O	Ribosomal protein US14	protein	127	27% helix, 20% strand	P27069
P	Ribosomal protein US19	protein	123	29% helix, 13% strand	Q6CKV4
Q	Ribosomal protein US9	protein	141	36% helix, 21% strand	Q875N2
R	Ribosomal protein ES17	protein	129	49% helix, 2% strand	Q6CWU3
S	Ribosomal protein US13	protein	145	38% helix, 5% strand	Q6CWT9
T	Ribosomal protein ES19	protein	143	48% helix, 8% strand	Q6CXM0
U	Ribosomal protein US10	protein	106	25% helix, 42% strand	Q6CIM1
V	Ribosomal protein ES21	protein	87	21% helix, 18% strand	Q6CXT6
W	Ribosomal protein US8	protein	129	34% helix, 22% strand	Q6CW21
X	Ribosomal protein US21	protein	145	23% helix, 26% strand	Q875M3
Y	Ribosomal protein ES24	protein	134	41% helix, 26% strand	Q6CU44
Z	Ribosomal protein ES25	protein	70	33% helix, 10% strand	Q6CW78
a	Ribosomal protein ES26	protein	100	17% helix, 20% strand	Q6CS01
b	Ribosomal protein ES27	protein	82	7% helix, 22% strand	Q6CNL2
c	Ribosomal protein ES28	protein	63	0% helix, 46% strand	P33285
d	Ribosomal protein ES29	protein	53	19% helix, 11% strand	Q6CPG3
e	Ribosomal protein ES30	protein	55	33% helix, 0% strand	Q6CUH5
f	Ribosomal protein ES31	protein	69	0% helix, 14% strand	P69061
g	Ribosomal protein RACK1	protein	318	0% helix, 51% strand	Q6CNI7
2	18S ribosomal RNA	rna	1780	—	—
i	Cricket paralysis virus ires RNA	rna	192	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 80 copies · chains G, 2, N, T, X, i, a, E, D, I, Q, S
ZN · Zinc ion · metal · 3 copies · chains a, b, f

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1158	0.89	0.91	93	MG
2	942	0.88	0.91	91	MG
3	815	0.88	0.92	88	empty
4	716	0.88	0.93	79	MG
5	998	0.88	0.90	84	MG

Interfaces

103 interfaces between chains.

G–2 · 5677 Å² buried · 130 hydrogen bonds · protein-nucleic
E–2 · 4458 Å² buried · 84 hydrogen bonds · protein-nucleic
I–2 · 4312 Å² buried · 121 hydrogen bonds · protein-nucleic
X–2 · 4002 Å² buried · 90 hydrogen bonds · protein-nucleic
J–2 · 3648 Å² buried · 61 hydrogen bonds · protein-nucleic

Compared structures

5IT9 · Structure of the yeast Kluyveromyces lactis small ribosomal subunit in complex with the… · the same entry in another collection · chain J against J, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q6CN12
Every structure of UniProt Q6CWD0
Every structure of UniProt Q6CKL3
Every structure of UniProt Q6CRK7
Every structure of UniProt Q6CWJ2
Every structure of UniProt Q6CRA3
Every structure of UniProt Q6CM04
Every structure of UniProt Q6CTD6
Every structure of UniProt Q6CMG3
Every structure of UniProt Q6CM18
Every structure of UniProt Q6CVZ5
Every structure of UniProt Q6CX80
Every structure of UniProt Q6CLU4
Every structure of UniProt Q6CJK0
Every structure of UniProt P27069
Every structure of UniProt Q6CKV4
Every structure of UniProt Q875N2
Every structure of UniProt Q6CWU3
Every structure of UniProt Q6CWT9
Every structure of UniProt Q6CXM0
Every structure of UniProt Q6CIM1
Every structure of UniProt Q6CXT6
Every structure of UniProt Q6CW21
Every structure of UniProt Q875M3
Every structure of UniProt Q6CU44
Every structure of UniProt Q6CW78
Every structure of UniProt Q6CS01
Every structure of UniProt Q6CNL2
Every structure of UniProt P33285
Every structure of UniProt Q6CPG3
Every structure of UniProt Q6CUH5
Every structure of UniProt P69061
Every structure of UniProt Q6CNI7
Elsewhere: RCSB PDB 5IT9 · PDBe 5IT9 · UniProt Q6CN12 · UniProt Q6CWD0 · UniProt Q6CKL3 · UniProt Q6CRK7 · UniProt Q6CWJ2 · UniProt Q6CRA3 · UniProt Q6CM04 · UniProt Q6CTD6 · UniProt Q6CMG3 · UniProt Q6CM18 · UniProt Q6CVZ5 · UniProt Q6CX80 · UniProt Q6CLU4 · UniProt Q6CJK0 · UniProt P27069 · UniProt Q6CKV4 · UniProt Q875N2 · UniProt Q6CWU3 · UniProt Q6CWT9 · UniProt Q6CXM0 · UniProt Q6CIM1 · UniProt Q6CXT6 · UniProt Q6CW21 · UniProt Q875M3 · UniProt Q6CU44 · UniProt Q6CW78 · UniProt Q6CS01 · UniProt Q6CNL2 · UniProt P33285 · UniProt Q6CPG3 · UniProt Q6CUH5 · UniProt P69061 · UniProt Q6CNI7

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