Research workbench

RBGA+45SRBGA complex

Analyse RBGA+45SRBGA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6PPK
Type: protein + RNA
Length: 5,454 residues
Chains: 24
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 23S rRNA; 5S rRNA; 50S ribosomal protein L2; 50S ribosomal protein L3; 50S ribosomal…
UniProt: A0A063XCB6, A0A063X745, A0A063X8U6, A0A063XB64, A0A063X781, A0A063XCH0, A0A063X754, A0A063XCP1, A0A063XCG5, F5HRS9, A0A063XHU6, A0A063XFC1, A0A063XIS2, F5HRT3, A0A063XB36, F5HRS7, A0A063XF22, F5HRU6, A0A3A5I502, F5HRV8, A0A063XCT1, A0A164SGC3
Ligands: GNP
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 24 distinct chains · 23% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	23S rRNA	rna	2658	—	—
B	5S rRNA	rna	112	—	—
C	50S ribosomal protein L2	protein	260	10% helix, 28% strand	A0A063XCB6
D	50S ribosomal protein L3	protein	206	7% helix, 31% strand	A0A063X745
E	50S ribosomal protein L4	protein	197	31% helix, 10% strand	A0A063X8U6
F	50S ribosomal protein L5	protein	139	19% helix, 14% strand	A0A063XB64
G	50S ribosomal protein L6	protein	109	30% helix, 24% strand	A0A063X781
J	50S ribosomal protein L13	protein	141	28% helix, 12% strand	A0A063XCH0
K	50S ribosomal protein L14	protein	122	0% helix, 37% strand	A0A063X754
L	50S ribosomal protein L15	protein	122	11% helix, 11% strand	A0A063XCP1
N	50S ribosomal protein L17	protein	118	47% helix, 21% strand	A0A063XCG5
O	50S ribosomal protein L18	protein	100	34% helix, 9% strand	F5HRS9
P	50S ribosomal protein L19	protein	114	18% helix, 34% strand	A0A063XHU6
Q	50S ribosomal protein L20	protein	117	64% helix, 0% strand	A0A063XFC1
R	50S ribosomal protein L21	protein	100	0% helix, 44% strand	A0A063XIS2
S	50S ribosomal protein L22	protein	109	33% helix, 26% strand	F5HRT3
T	50S ribosomal protein L23	protein	90	18% helix, 24% strand	A0A063XB36
U	50S ribosomal protein L24	protein	91	7% helix, 30% strand	F5HRS7
V	50S ribosomal protein L27	protein	78	0% helix, 36% strand	A0A063XF22
Z	50S ribosomal protein L30	protein	58	33% helix, 26% strand	F5HRU6
b	50S ribosomal protein L32	protein	53	8% helix, 11% strand	A0A3A5I502
Y	50S ribosomal protein L29	protein	65	75% helix, 0% strand	F5HRV8
d	50S ribosomal protein L34	protein	43	47% helix, 0% strand	A0A063XCT1
W	Ribosome biogenesis GTPase a	protein	252	32% helix, 9% strand	A0A164SGC3

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A, W

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	861	0.87	0.90	67	empty
2	705	0.86	0.91	79	empty
3	943	0.86	0.88	81	empty
4	786	0.85	0.89	73	empty
5	951	0.85	0.87	105	GNP

Interfaces

42 interfaces between chains.

A–C · 6408 Å² buried · 169 hydrogen bonds · protein-nucleic
A–D · 5100 Å² buried · 116 hydrogen bonds · protein-nucleic
A–Q · 4373 Å² buried · 103 hydrogen bonds · protein-nucleic
A–E · 4361 Å² buried · 84 hydrogen bonds · protein-nucleic
A–L · 3238 Å² buried · 82 hydrogen bonds · protein-nucleic

Compared structures

6PPK · RbgA+45SRbgA complex · the same entry in another collection · chain A against A, 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 A0A063XCB6
Every structure of UniProt A0A063X745
Every structure of UniProt A0A063X8U6
Every structure of UniProt A0A063XB64
Every structure of UniProt A0A063X781
Every structure of UniProt A0A063XCH0
Every structure of UniProt A0A063X754
Every structure of UniProt A0A063XCP1
Every structure of UniProt A0A063XCG5
Every structure of UniProt F5HRS9
Every structure of UniProt A0A063XHU6
Every structure of UniProt A0A063XFC1
Every structure of UniProt A0A063XIS2
Every structure of UniProt F5HRT3
Every structure of UniProt A0A063XB36
Every structure of UniProt F5HRS7
Every structure of UniProt A0A063XF22
Every structure of UniProt F5HRU6
Every structure of UniProt A0A3A5I502
Every structure of UniProt F5HRV8
Every structure of UniProt A0A063XCT1
Every structure of UniProt A0A164SGC3
Elsewhere: RCSB PDB 6PPK · PDBe 6PPK · UniProt A0A063XCB6 · UniProt A0A063X745 · UniProt A0A063X8U6 · UniProt A0A063XB64 · UniProt A0A063X781 · UniProt A0A063XCH0 · UniProt A0A063X754 · UniProt A0A063XCP1 · UniProt A0A063XCG5 · UniProt F5HRS9 · UniProt A0A063XHU6 · UniProt A0A063XFC1 · UniProt A0A063XIS2 · UniProt F5HRT3 · UniProt A0A063XB36 · UniProt F5HRS7 · UniProt A0A063XF22 · UniProt F5HRU6 · UniProt A0A3A5I502 · UniProt F5HRV8 · UniProt A0A063XCT1 · UniProt A0A164SGC3

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