Research workbench

Large subunit of mycobacterium smegmatis

Analyse Large subunit of mycobacterium smegmatis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5XYM
Type: protein + RNA
Length: 5,903 residues
Chains: 31
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 50S ribosomal protein L32; 50S ribosomal protein L33 2; 50S ribosomal protein L34; 50S…
UniProt: A0R3I9, A0R551, A0R7K0, A0QYU7, A0QSL4, A0QSD4, A0QSD1, A0QSD2, A0QSG1, A0QSG4, A0R7F6, A0QSP8, A0QSF9, I7G436, A0QSD8, A0QSL9, I7FGD9, A0QV42, A0QYU6, A0R151, A0QSD6, A0QSD3, A0QSG0, I7GFB2, A0R150, I7FJ52, A0QSD9, A0QSG7, A0QTP4
Ligands: MG
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 31 distinct chains · 24% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0	50S ribosomal protein L32	protein	55	31% helix, 4% strand	A0R3I9
1	50S ribosomal protein L33 2	protein	44	0% helix, 30% strand	A0R551
2	50S ribosomal protein L34	protein	46	57% helix, 0% strand	A0R7K0
3	50S ribosomal protein L35	protein	63	30% helix, 6% strand	A0QYU7
4	50S ribosomal protein L36	protein	37	0% helix, 22% strand	A0QSL4
A	23S RNA	rna	2665	—	—
B	5S RNA	rna	116	—	—
C	50S ribosomal protein L2	protein	273	3% helix, 21% strand	A0QSD4
D	50S ribosomal protein L3	protein	212	12% helix, 34% strand	A0QSD1
E	50S ribosomal protein L4	protein	208	32% helix, 10% strand	A0QSD2
F	50S ribosomal protein L5	protein	174	33% helix, 18% strand	A0QSG1
G	50S ribosomal protein L6	protein	139	24% helix, 24% strand	A0QSG4
H	50S ribosomal protein L9	protein	34	32% helix, 15% strand	A0R7F6
J	50S ribosomal protein L13	protein	146	27% helix, 16% strand	A0QSP8
K	50S ribosomal protein L14	protein	122	8% helix, 31% strand	A0QSF9
L	50S ribosomal protein L15	protein	144	20% helix, 13% strand	I7G436
M	50S ribosomal protein L16	protein	134	20% helix, 22% strand	A0QSD8
N	50S ribosomal protein L17	protein	116	51% helix, 17% strand	A0QSL9
O	50S ribosomal protein L18	protein	107	42% helix, 22% strand	I7FGD9
P	50S ribosomal protein L19	protein	111	9% helix, 37% strand	A0QV42
Q	50S ribosomal protein L20	protein	124	69% helix, 0% strand	A0QYU6
R	50S ribosomal protein L21	protein	100	4% helix, 52% strand	A0R151
S	50S ribosomal protein L22	protein	111	31% helix, 30% strand	A0QSD6
T	50S ribosomal protein L23	protein	91	25% helix, 22% strand	A0QSD3
U	50S ribosomal protein L24	protein	83	4% helix, 37% strand	A0QSG0
V	50S ribosomal protein L25	protein	168	14% helix, 40% strand	I7GFB2
W	50S ribosomal protein L27	protein	76	0% helix, 26% strand	A0R150
X	50S ribosomal protein L28	protein	62	8% helix, 29% strand	I7FJ52
Y	50S ribosomal protein L29	protein	61	72% helix, 0% strand	A0QSD9
Z	50S ribosomal protein L30	protein	58	33% helix, 21% strand	A0QSG7
a	Uncharacterized protein BL37	protein	23	48% helix, 0% strand	A0QTP4

Ligands and binding sites

MG · Magnesium ion · metal · 146 copies · chains A, E, Q, C, L, N, 0, D, T, J, X, M, a

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	1077	0.88	0.90	96	MG
2	597	0.87	0.93	74	MG
3	787	0.87	0.91	82	MG
4	783	0.86	0.90	79	MG
5	645	0.86	0.91	77	MG

Interfaces

56 interfaces between chains.

A–C · 7322 Å² buried · 145 hydrogen bonds · protein-nucleic
A–D · 5056 Å² buried · 98 hydrogen bonds · protein-nucleic
A–L · 4563 Å² buried · 91 hydrogen bonds · protein-nucleic
A–Q · 4517 Å² buried · 104 hydrogen bonds · protein-nucleic
A–E · 4429 Å² buried · 83 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

5XYM · Large subunit of Mycobacterium smegmatis · the same entry in another collection · chain D against D, 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 A0R3I9
Every structure of UniProt A0R551
Every structure of UniProt A0R7K0
Every structure of UniProt A0QYU7
Every structure of UniProt A0QSL4
Every structure of UniProt A0QSD4
Every structure of UniProt A0QSD1
Every structure of UniProt A0QSD2
Every structure of UniProt A0QSG1
Every structure of UniProt A0QSG4
Every structure of UniProt A0R7F6
Every structure of UniProt A0QSP8
Every structure of UniProt A0QSF9
Every structure of UniProt I7G436
Every structure of UniProt A0QSD8
Every structure of UniProt A0QSL9
Every structure of UniProt I7FGD9
Every structure of UniProt A0QV42
Every structure of UniProt A0QYU6
Every structure of UniProt A0R151
Every structure of UniProt A0QSD6
Every structure of UniProt A0QSD3
Every structure of UniProt A0QSG0
Every structure of UniProt I7GFB2
Every structure of UniProt A0R150
Every structure of UniProt I7FJ52
Every structure of UniProt A0QSD9
Every structure of UniProt A0QSG7
Every structure of UniProt A0QTP4
Elsewhere: RCSB PDB 5XYM · PDBe 5XYM · UniProt A0R3I9 · UniProt A0R551 · UniProt A0R7K0 · UniProt A0QYU7 · UniProt A0QSL4 · UniProt A0QSD4 · UniProt A0QSD1 · UniProt A0QSD2 · UniProt A0QSG1 · UniProt A0QSG4 · UniProt A0R7F6 · UniProt A0QSP8 · UniProt A0QSF9 · UniProt I7G436 · UniProt A0QSD8 · UniProt A0QSL9 · UniProt I7FGD9 · UniProt A0QV42 · UniProt A0QYU6 · UniProt A0R151 · UniProt A0QSD6 · UniProt A0QSD3 · UniProt A0QSG0 · UniProt I7GFB2 · UniProt A0R150 · UniProt I7FJ52 · UniProt A0QSD9 · UniProt A0QSG7 · UniProt A0QTP4

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