Research workbench

Improved model derived from cryo-EM map of Staphylococcus aureus large ribosomal subunit

Analyse Improved model derived from cryo-EM map of Staphylococcus aureus large… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6HMA
Type: protein + RNA
Length: 5,988 residues
Chains: 29
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.65
Source: Staphylococcus aureus
Molecule: 23S ribosomal RNA; 5S ribosomal RNA; 50S ribosomal protein L2; 50S ribosomal protein L3…
UniProt: Q2YYP9, Q2YYP6, Q2YYP7, A0A2S6D0C0, Q2YYL2, Q2YYM8, Q2YYK7, Q2YYL6, Q2YYQ3, Q2YYM3, W8TRE0, Q2YXM4, Q2YTB1, Q2YT83, Q2YYQ1, Q2YYP8, Q2YYK8, A0A133Q8Z9, Q2YT85, Q2YXJ2, Q2YYN0, Q2YYL5, A0A1Q8DAT0, A0A077V2P0, Q2YZB6, Q2YTB0, A0A077UGV8
Ligands: MG
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · resolution 2.65 · 29 distinct chains · 22% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	23S ribosomal RNA	rna	2834	—	—
B	5S ribosomal RNA	rna	115	—	—
C	50S ribosomal protein L2	protein	274	9% helix, 26% strand	Q2YYP9
D	50S ribosomal protein L3	protein	215	9% helix, 34% strand	Q2YYP6
E	50S ribosomal protein L4	protein	206	32% helix, 15% strand	Q2YYP7
F	50S ribosomal protein L5	protein	158	25% helix, 9% strand	A0A2S6D0C0
G	50S ribosomal protein L6	protein	175	19% helix, 32% strand	Q2YYL2
H	50S ribosomal protein L13	protein	145	26% helix, 17% strand	Q2YYM8
I	50S ribosomal protein L14	protein	122	10% helix, 34% strand	Q2YYK7
J	50S ribosomal protein L15	protein	146	16% helix, 8% strand	Q2YYL6
K	50S ribosomal protein L16	protein	137	18% helix, 23% strand	Q2YYQ3
L	50S ribosomal protein L17	protein	120	48% helix, 20% strand	Q2YYM3
M	50S ribosomal protein L18	protein	119	32% helix, 18% strand	W8TRE0
N	50S ribosomal protein L19	protein	114	18% helix, 36% strand	Q2YXM4
O	50S ribosomal protein L20	protein	116	75% helix, 0% strand	Q2YTB1
P	50S ribosomal protein L21	protein	102	0% helix, 57% strand	Q2YT83
Q	50S ribosomal protein L22	protein	112	29% helix, 35% strand	Q2YYQ1
R	50S ribosomal protein L23	protein	89	19% helix, 40% strand	Q2YYP8
S	50S ribosomal protein L24	protein	103	6% helix, 32% strand	Q2YYK8
T	50S ribosomal protein L25	protein	94	22% helix, 47% strand	A0A133Q8Z9
U	50S ribosomal protein L27	protein	79	0% helix, 37% strand	Q2YT85
V	50S ribosomal protein L28	protein	49	8% helix, 41% strand	Q2YXJ2
W	50S ribosomal protein L29	protein	67	67% helix, 0% strand	Q2YYN0
X	50S ribosomal protein L30	protein	58	33% helix, 24% strand	Q2YYL5
Z	50S ribosomal protein L32	protein	48	15% helix, 8% strand	A0A1Q8DAT0
1	50S ribosomal protein L33	protein	47	0% helix, 51% strand	A0A077V2P0
2	50S ribosomal protein L34	protein	43	56% helix, 0% strand	Q2YZB6
3	50S ribosomal protein L35	protein	64	25% helix, 13% strand	Q2YTB0
4	50S ribosomal protein L36	protein	37	8% helix, 38% strand	A0A077UGV8

Ligands and binding sites

MG · Magnesium ion · metal · 237 copies · chains A, O, E, J, C, H, R, D, L, Q, B, K, U, Z

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	984	0.89	0.91	85	MG
2	768	0.89	0.93	94	MG
3	957	0.88	0.90	100	MG
4	978	0.87	0.89	97	MG
5	805	0.86	0.90	84	MG

Interfaces

54 interfaces between chains.

A–C · 6805 Å² buried · 120 hydrogen bonds · protein-nucleic
A–D · 4911 Å² buried · 85 hydrogen bonds · protein-nucleic
A–J · 4338 Å² buried · 75 hydrogen bonds · protein-nucleic
A–E · 4233 Å² buried · 64 hydrogen bonds · protein-nucleic
A–O · 3905 Å² buried · 77 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 3 disulfide, 3 modified (disulfide, nucleotide modification).

Compared structures

6HMA · Improved model derived from cryo-EM MAP of staphylococcus aureus large ribosomal subunit · the same entry in another collection · chain E against E, 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 Q2YYP9
Every structure of UniProt Q2YYP6
Every structure of UniProt Q2YYP7
Every structure of UniProt A0A2S6D0C0
Every structure of UniProt Q2YYL2
Every structure of UniProt Q2YYM8
Every structure of UniProt Q2YYK7
Every structure of UniProt Q2YYL6
Every structure of UniProt Q2YYQ3
Every structure of UniProt Q2YYM3
Every structure of UniProt W8TRE0
Every structure of UniProt Q2YXM4
Every structure of UniProt Q2YTB1
Every structure of UniProt Q2YT83
Every structure of UniProt Q2YYQ1
Every structure of UniProt Q2YYP8
Every structure of UniProt Q2YYK8
Every structure of UniProt A0A133Q8Z9
Every structure of UniProt Q2YT85
Every structure of UniProt Q2YXJ2
Every structure of UniProt Q2YYN0
Every structure of UniProt Q2YYL5
Every structure of UniProt A0A1Q8DAT0
Every structure of UniProt A0A077V2P0
Every structure of UniProt Q2YZB6
Every structure of UniProt Q2YTB0
Every structure of UniProt A0A077UGV8
Elsewhere: RCSB PDB 6HMA · PDBe 6HMA · UniProt Q2YYP9 · UniProt Q2YYP6 · UniProt Q2YYP7 · UniProt A0A2S6D0C0 · UniProt Q2YYL2 · UniProt Q2YYM8 · UniProt Q2YYK7 · UniProt Q2YYL6 · UniProt Q2YYQ3 · UniProt Q2YYM3 · UniProt W8TRE0 · UniProt Q2YXM4 · UniProt Q2YTB1 · UniProt Q2YT83 · UniProt Q2YYQ1 · UniProt Q2YYP8 · UniProt Q2YYK8 · UniProt A0A133Q8Z9 · UniProt Q2YT85 · UniProt Q2YXJ2 · UniProt Q2YYN0 · UniProt Q2YYL5 · UniProt A0A1Q8DAT0 · UniProt A0A077V2P0 · UniProt Q2YZB6 · UniProt Q2YTB0 · UniProt A0A077UGV8

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