MolNFT v1 · #121087 · protein + RNA

The crystal structure of the large ribosomal subunit of staphylococcus aureus in complex with lincomycin

5HKV · 23S ribosomal RNA: “The crystal structure of the large ribosomal subunit of staphylococcus aureus in complex with lincomycin”. X-ray diffraction, 5 ligands (SPD, 3QB, MN), 20 pockets (best druggability 0.89). MolNFT v1 #121087 on…

PDB: 5HKV
Type: protein + RNA
Length: 5,760 residues
Chains: 27
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 23S ribosomal RNA; 5S ribosomal RNA; 50S ribosomal protein L2; 50S ribosomal protein L3…
UniProt: P60430, Q2FW06, Q2FW07, Q2FW18, Q2FW21, Q2FW38, Q2FW16, P0A0F8, Q2FW13, Q2FW33, Q2FW22, Q2FZ42, Q2FXQ1, Q2FXS8, Q2FW11, Q2FW08, Q2FW17, Q2FJE0, Q2FXT0, Q2FZ60, Q2FW14, P0A0G2, Q2FZF1, Q2FUQ0, Q2FXQ0
Ligands: SPD, 3QB, MN, MG, CA
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 27 distinct chains · 21% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X	23S ribosomal RNA	rna	2695	—	—
Y	5S ribosomal RNA	rna	114	—	—
A	50S ribosomal protein L2	protein	269	1% helix, 15% strand	P60430
B	50S ribosomal protein L3	protein	215	7% helix, 32% strand	Q2FW06
C	50S ribosomal protein L4	protein	199	26% helix, 9% strand	Q2FW07
D	50S ribosomal protein L5	protein	166	25% helix, 11% strand	Q2FW18
E	50S ribosomal protein L6	protein	158	18% helix, 9% strand	Q2FW21
G	50S ribosomal protein L13	protein	145	29% helix, 13% strand	Q2FW38
H	50S ribosomal protein L14	protein	122	7% helix, 34% strand	Q2FW16
I	50S ribosomal protein L15	protein	131	10% helix, 8% strand	P0A0F8
J	50S ribosomal protein L16	protein	137	19% helix, 25% strand	Q2FW13
K	50S ribosomal protein L17	protein	119	49% helix, 18% strand	Q2FW33
L	50S ribosomal protein L18	protein	109	33% helix, 7% strand	Q2FW22
M	50S ribosomal protein L19	protein	108	11% helix, 34% strand	Q2FZ42
N	50S ribosomal protein L20	protein	116	76% helix, 0% strand	Q2FXQ1
O	50S ribosomal protein L21	protein	102	0% helix, 47% strand	Q2FXS8
P	50S ribosomal protein L22	protein	112	38% helix, 38% strand	Q2FW11
Q	50S ribosomal protein L23	protein	89	19% helix, 24% strand	Q2FW08
R	50S ribosomal protein L24	protein	101	3% helix, 20% strand	Q2FW17
S	50S ribosomal protein L25	protein	167	10% helix, 32% strand	Q2FJE0
T	50S ribosomal protein L27	protein	75	0% helix, 36% strand	Q2FXT0
U	50S ribosomal protein L28	protein	42	0% helix, 29% strand	Q2FZ60
V	50S ribosomal protein L29	protein	65	74% helix, 0% strand	Q2FW14
W	50S ribosomal protein L30	protein	57	37% helix, 21% strand	P0A0G2
Z	50S ribosomal protein L32	protein	43	23% helix, 14% strand	Q2FZF1
2	50S ribosomal protein L34	protein	44	52% helix, 0% strand	Q2FUQ0
3	50S ribosomal protein L35	protein	60	18% helix, 10% strand	Q2FXQ0

Ligands and binding sites

SPD · Spermidine · ligand · 9 copies · chains X, G, Y
3QB · Lincomycin · ligand · chains X
MN · Manganese (II) ion · metal · 338 copies · chains X, G, B, N, C, I, M, 2, A, T, Y, S, J, R, Z
MG · Magnesium ion · metal · 162 copies · chains X, A, 2, J, N, Q, L, E, 3, Y, B, G, O, K, M, P, R, S, T, I
CA · Calcium ion · metal · chains Y
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 24 copies · chains X, U, M, T, J, S
EOH · Ethanol · additive · 9 copies · chains X, I, C, R

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	842	0.89	0.92	86	MN, MG
2	1079	0.88	0.90	117	MG, MN
3	1006	0.88	0.90	105	empty
4	1196	0.86	0.88	128	MG, MN, EOH
5	1108	0.86	0.88	96	MG, MN

Interfaces

51 interfaces between chains.

X–A · 5598 Å² buried · 100 hydrogen bonds · protein-nucleic
X–B · 5004 Å² buried · 115 hydrogen bonds · protein-nucleic
X–C · 3956 Å² buried · 73 hydrogen bonds · protein-nucleic
X–N · 3780 Å² buried · 109 hydrogen bonds · protein-nucleic
X–I · 3186 Å² buried · 56 hydrogen bonds · protein-nucleic

Compared structures

5HKV · The crystal structure of the large ribosomal subunit of Staphylococcus aureus in complex… · 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 P60430
Every structure of UniProt Q2FW06
Every structure of UniProt Q2FW07
Every structure of UniProt Q2FW18
Every structure of UniProt Q2FW21
Every structure of UniProt Q2FW38
Every structure of UniProt Q2FW16
Every structure of UniProt P0A0F8
Every structure of UniProt Q2FW13
Every structure of UniProt Q2FW33
Every structure of UniProt Q2FW22
Every structure of UniProt Q2FZ42
Every structure of UniProt Q2FXQ1
Every structure of UniProt Q2FXS8
Every structure of UniProt Q2FW11
Every structure of UniProt Q2FW08
Every structure of UniProt Q2FW17
Every structure of UniProt Q2FJE0
Every structure of UniProt Q2FXT0
Every structure of UniProt Q2FZ60
Every structure of UniProt Q2FW14
Every structure of UniProt P0A0G2
Every structure of UniProt Q2FZF1
Every structure of UniProt Q2FUQ0
Every structure of UniProt Q2FXQ0
Elsewhere: RCSB PDB 5HKV · PDBe 5HKV · UniProt P60430 · UniProt Q2FW06 · UniProt Q2FW07 · UniProt Q2FW18 · UniProt Q2FW21 · UniProt Q2FW38 · UniProt Q2FW16 · UniProt P0A0F8 · UniProt Q2FW13 · UniProt Q2FW33 · UniProt Q2FW22 · UniProt Q2FZ42 · UniProt Q2FXQ1 · UniProt Q2FXS8 · UniProt Q2FW11 · UniProt Q2FW08 · UniProt Q2FW17 · UniProt Q2FJE0 · UniProt Q2FXT0 · UniProt Q2FZ60 · UniProt Q2FW14 · UniProt P0A0G2 · UniProt Q2FZF1 · UniProt Q2FUQ0 · UniProt Q2FXQ0

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