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Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit

Analyse Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3PIO
Type: protein + RNA
Length: 5,944 residues
Chains: 30
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribosomal 23S RNA; 5S ribosomal RNA; 50S ribosomal protein L2; 50S ribosomal protein L3…
UniProt: Q9RXJ9, Q9RXK2, Q9RXK1, Q9RXJ0, Q9RSL3, Q9RSS7, Q9RXY1, Q9RXJ2, Q9RSK9, Q9RXJ5, Q9RSJ5, Q9RSL2, Q9RWB4, Q9RSW7, Q9RY64, Q9RXJ7, Q9RXK0, Q9RXJ1, Q9RX88, Q9RY65, Q9RRG8, Q9RXJ4, Q9RSL0, P49228, Q9RSS4, Q9RSH2, Q9RSW6, Q9RSK0
Ligands: LMA, MG, NA, K
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 30 distinct chains · 20% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X	Ribosomal 23S RNA	rna	2657	—	—
Y	5S ribosomal RNA	rna	120	—	—
A	50S ribosomal protein L2	protein	253	4% helix, 22% strand	Q9RXJ9
B	50S ribosomal protein L3	protein	205	8% helix, 36% strand	Q9RXK2
C	50S ribosomal protein L4	protein	194	25% helix, 5% strand	Q9RXK1
D	50S ribosomal protein L5	protein	177	28% helix, 18% strand	Q9RXJ0
E	50S ribosomal protein L6	protein	171	18% helix, 30% strand	Q9RSL3
F	50S ribosomal protein L11	protein	63	46% helix, 0% strand	Q9RSS7
G	50S ribosomal protein L13	protein	142	26% helix, 15% strand	Q9RXY1
H	50S ribosomal protein L14	protein	134	7% helix, 39% strand	Q9RXJ2
I	50S ribosomal protein L15	protein	134	13% helix, 9% strand	Q9RSK9
J	50S ribosomal protein L16	protein	136	18% helix, 19% strand	Q9RXJ5
K	50S ribosomal protein L17	protein	113	52% helix, 12% strand	Q9RSJ5
L	50S ribosomal protein L18	protein	104	31% helix, 11% strand	Q9RSL2
M	50S ribosomal protein L19	protein	108	9% helix, 39% strand	Q9RWB4
N	50S ribosomal protein L20	protein	117	71% helix, 0% strand	Q9RSW7
O	50S ribosomal protein L21	protein	94	4% helix, 35% strand	Q9RY64
P	50S ribosomal protein L22	protein	126	32% helix, 31% strand	Q9RXJ7
Q	50S ribosomal protein L23	protein	93	18% helix, 29% strand	Q9RXK0
R	50S ribosomal protein L24	protein	110	0% helix, 20% strand	Q9RXJ1
S	50S ribosomal protein L25	protein	175	8% helix, 31% strand	Q9RX88
T	50S ribosomal protein L27	protein	74	0% helix, 41% strand	Q9RY65
U	50S ribosomal protein L28	protein	72	13% helix, 11% strand	Q9RRG8
V	50S ribosomal protein L29	protein	65	72% helix, 0% strand	Q9RXJ4
W	50S ribosomal protein L30	protein	55	25% helix, 15% strand	Q9RSL0
Z	50S ribosomal protein L32	protein	57	12% helix, 14% strand	P49228
1	50S ribosomal protein L33	protein	53	0% helix, 23% strand	Q9RSS4
2	50S ribosomal protein L34	protein	46	41% helix, 0% strand	Q9RSH2
3	50S ribosomal protein L35	protein	59	15% helix, 3% strand	Q9RSW6
4	50S ribosomal protein L36	protein	37	8% helix, 30% strand	Q9RSK0

Ligands and binding sites

LMA · Lankamycin · ligand · chains X, P
MG · Magnesium ion · metal · 154 copies · chains X, B, K, O, A, C, I, Y, Q, N, 3, U
NA · Sodium ion · metal · 42 copies · chains X, Y, Z, 3, A, K
K · Potassium ion · metal · 15 copies · chains X, M

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	1080	0.89	0.91	89	MG
2	1050	0.87	0.90	92	MG
3	774	0.87	0.91	85	MG
4	768	0.87	0.91	73	MG
5	1197	0.87	0.89	88	MG, NA, K

Interfaces

58 interfaces between chains.

X–A · 6543 Å² buried · 130 hydrogen bonds · protein-nucleic
X–B · 5089 Å² buried · 122 hydrogen bonds · protein-nucleic
X–N · 4264 Å² buried · 78 hydrogen bonds · protein-nucleic
X–C · 4258 Å² buried · 76 hydrogen bonds · protein-nucleic
X–I · 3881 Å² buried · 66 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

3PIO · Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex… · the same entry in another collection · chain I against I, 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 Q9RXJ9
Every structure of UniProt Q9RXK2
Every structure of UniProt Q9RXK1
Every structure of UniProt Q9RXJ0
Every structure of UniProt Q9RSL3
Every structure of UniProt Q9RSS7
Every structure of UniProt Q9RXY1
Every structure of UniProt Q9RXJ2
Every structure of UniProt Q9RSK9
Every structure of UniProt Q9RXJ5
Every structure of UniProt Q9RSJ5
Every structure of UniProt Q9RSL2
Every structure of UniProt Q9RWB4
Every structure of UniProt Q9RSW7
Every structure of UniProt Q9RY64
Every structure of UniProt Q9RXJ7
Every structure of UniProt Q9RXK0
Every structure of UniProt Q9RXJ1
Every structure of UniProt Q9RX88
Every structure of UniProt Q9RY65
Every structure of UniProt Q9RRG8
Every structure of UniProt Q9RXJ4
Every structure of UniProt Q9RSL0
Every structure of UniProt P49228
Every structure of UniProt Q9RSS4
Every structure of UniProt Q9RSH2
Every structure of UniProt Q9RSW6
Every structure of UniProt Q9RSK0
Elsewhere: RCSB PDB 3PIO · PDBe 3PIO · UniProt Q9RXJ9 · UniProt Q9RXK2 · UniProt Q9RXK1 · UniProt Q9RXJ0 · UniProt Q9RSL3 · UniProt Q9RSS7 · UniProt Q9RXY1 · UniProt Q9RXJ2 · UniProt Q9RSK9 · UniProt Q9RXJ5 · UniProt Q9RSJ5 · UniProt Q9RSL2 · UniProt Q9RWB4 · UniProt Q9RSW7 · UniProt Q9RY64 · UniProt Q9RXJ7 · UniProt Q9RXK0 · UniProt Q9RXJ1 · UniProt Q9RX88 · UniProt Q9RY65 · UniProt Q9RRG8 · UniProt Q9RXJ4 · UniProt Q9RSL0 · UniProt P49228 · UniProt Q9RSS4 · UniProt Q9RSH2 · UniProt Q9RSW6 · UniProt Q9RSK0

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