Research workbench

Acinetobacter baumannii ribosome-amikacin complex - 50S subunit

Analyse Acinetobacter baumannii ribosome-amikacin complex - 50S subunit in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YHS
Type: protein + RNA
Length: 5,869 residues
Chains: 31
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 23S ribosomal RNA; 5S ribosomal RNA; E-site tRNA; 50S ribosomal protein L2; 50S ribosomal…
UniProt: D0CD00, D0CCZ7, D0CCZ8, D0CD09, D0CD12, D0CG35, D0CD07, D0CD16, D0CD04, D0CD23, D0CD13, D0CCR8, D0CA76, D0CDQ6, D0CD02, D0CCZ9, D0CD08, D0C9L7, D0CDQ7, D0CAL0, D0CD05, D0CD15, D0C9K5, D0CAL1, D0CG06, D0CA77, D0CD18
Ligands: MG, ZN
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 31 distinct chains · 24% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	23S ribosomal RNA	rna	2672	—	—
5	5S ribosomal RNA	rna	115	—	—
6	E-site tRNA	rna	5	—	—
8	E-site tRNA	rna	8	—	—
A	50S ribosomal protein L2	protein	272	6% helix, 29% strand	D0CD00
B	50S ribosomal protein L3	protein	211	9% helix, 38% strand	D0CCZ7
C	50S ribosomal protein L4	protein	199	34% helix, 13% strand	D0CCZ8
D	50S ribosomal protein L5	protein	176	26% helix, 9% strand	D0CD09
E	50S ribosomal protein L6	protein	175	19% helix, 31% strand	D0CD12
F	50S ribosomal protein L13	protein	142	33% helix, 18% strand	D0CG35
G	50S ribosomal protein L14	protein	122	7% helix, 41% strand	D0CD07
H	50S ribosomal protein L15	protein	144	20% helix, 13% strand	D0CD16
I	50S ribosomal protein L16	protein	137	20% helix, 28% strand	D0CD04
J	50S ribosomal protein L17	protein	119	50% helix, 17% strand	D0CD23
K	50S ribosomal protein L18	protein	115	37% helix, 20% strand	D0CD13
L	50S ribosomal protein L19	protein	117	17% helix, 42% strand	D0CCR8
M	50S ribosomal protein L20	protein	117	78% helix, 0% strand	D0CA76
N	50S ribosomal protein L21	protein	103	0% helix, 64% strand	D0CDQ6
O	50S ribosomal protein L22	protein	109	38% helix, 36% strand	D0CD02
P	50S ribosomal protein L23	protein	92	32% helix, 36% strand	D0CCZ9
Q	50S ribosomal protein L24	protein	102	0% helix, 46% strand	D0CD08
R	50S ribosomal protein L25	protein	96	19% helix, 43% strand	D0C9L7
S	50S ribosomal protein L27	protein	76	0% helix, 41% strand	D0CDQ7
T	50S ribosomal protein L28	protein	77	30% helix, 36% strand	D0CAL0
U	50S ribosomal protein L29	protein	61	66% helix, 0% strand	D0CD05
V	50S ribosomal protein L30	protein	57	30% helix, 25% strand	D0CD15
X	50S ribosomal protein L32	protein	54	19% helix, 19% strand	D0C9K5
Y	50S ribosomal protein L33	protein	51	0% helix, 59% strand	D0CAL1
Z	50S ribosomal protein L34	protein	44	59% helix, 0% strand	D0CG06
a	50S ribosomal protein L35	protein	63	27% helix, 14% strand	D0CA77
b	50S ribosomal protein L36	protein	38	8% helix, 47% strand	D0CD18

Ligands and binding sites

MG · Magnesium ion · metal · 160 copies · chains 1, C, B, A, a, P, F, J, X, M, 5
ZN · Zinc ion · metal · chains b

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	824	0.88	0.92	63	MG
2	1059	0.88	0.90	117	MG
3	1104	0.88	0.90	95	MG
4	634	0.86	0.92	71	MG
5	635	0.86	0.91	72	MG

Interfaces

60 interfaces between chains.

1–A · 7030 Å² buried · 156 hydrogen bonds · protein-nucleic
1–B · 4953 Å² buried · 105 hydrogen bonds · protein-nucleic
1–H · 4675 Å² buried · 103 hydrogen bonds · protein-nucleic
1–M · 4034 Å² buried · 81 hydrogen bonds · protein-nucleic
1–C · 4022 Å² buried · 71 hydrogen bonds · protein-nucleic

Compared structures

6YHS · Acinetobacter baumannii ribosome-amikacin complex - 50S subunit · the same entry in another collection · chain 1 against 1, 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 D0CD00
Every structure of UniProt D0CCZ7
Every structure of UniProt D0CCZ8
Every structure of UniProt D0CD09
Every structure of UniProt D0CD12
Every structure of UniProt D0CG35
Every structure of UniProt D0CD07
Every structure of UniProt D0CD16
Every structure of UniProt D0CD04
Every structure of UniProt D0CD23
Every structure of UniProt D0CD13
Every structure of UniProt D0CCR8
Every structure of UniProt D0CA76
Every structure of UniProt D0CDQ6
Every structure of UniProt D0CD02
Every structure of UniProt D0CCZ9
Every structure of UniProt D0CD08
Every structure of UniProt D0C9L7
Every structure of UniProt D0CDQ7
Every structure of UniProt D0CAL0
Every structure of UniProt D0CD05
Every structure of UniProt D0CD15
Every structure of UniProt D0C9K5
Every structure of UniProt D0CAL1
Every structure of UniProt D0CG06
Every structure of UniProt D0CA77
Every structure of UniProt D0CD18
Elsewhere: RCSB PDB 6YHS · PDBe 6YHS · UniProt D0CD00 · UniProt D0CCZ7 · UniProt D0CCZ8 · UniProt D0CD09 · UniProt D0CD12 · UniProt D0CG35 · UniProt D0CD07 · UniProt D0CD16 · UniProt D0CD04 · UniProt D0CD23 · UniProt D0CD13 · UniProt D0CCR8 · UniProt D0CA76 · UniProt D0CDQ6 · UniProt D0CD02 · UniProt D0CCZ9 · UniProt D0CD08 · UniProt D0C9L7 · UniProt D0CDQ7 · UniProt D0CAL0 · UniProt D0CD05 · UniProt D0CD15 · UniProt D0C9K5 · UniProt D0CAL1 · UniProt D0CG06 · UniProt D0CA77 · UniProt D0CD18

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