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Co-crystal structure of spiramycin bound to the 50S ribosomal subunit of haloarcula marismortui

Analyse Co-crystal structure of spiramycin bound to the 50S ribosomal subunit of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1KD1
Type: protein + RNA
Length: 6,577 residues
Chains: 30
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 23S rRNA; 5S rRNA; Ribosomal protein L2; Ribosomal protein L3; Ribosomal protein L4…
UniProt: P20276, P20279, P12735, P14124, P14135, P12743, P15825, P29198, P22450, P12737, P14123, P12733, P14119, P12734, P10970, P12732, P10972, P14116, P10971, P14121, P18138, P12736, P32410, P22452, P32411
Ligands: SPR, MG, NA, CD, K, CL
Pockets: 20 · best druggability 0.90

Structure

x-ray diffraction · 30 distinct chains · 29% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	23S rRNA	rna	2754	—	—
B	5S rRNA	rna	122	—	—
C	Ribosomal protein L2	protein	237	12% helix, 24% strand	P20276
D	Ribosomal protein L3	protein	337	14% helix, 32% strand	P20279
E	Ribosomal protein L4	protein	246	33% helix, 15% strand	P12735
F	Ribosomal protein L5	protein	140	26% helix, 21% strand	P14124
G	Ribosomal protein L6	protein	172	22% helix, 41% strand	P14135
H	Ribosomal protein L7AE	protein	119	48% helix, 13% strand	P12743
I	Ribosomal protein L10	protein	29	79% helix, 0% strand	P15825
J	Ribosomal protein L10E	protein	156	13% helix, 28% strand	—
K	Ribosomal protein L13	protein	142	40% helix, 15% strand	P29198
L	Ribosomal protein L14	protein	132	5% helix, 38% strand	P22450
M	Ribosomal protein L15	protein	145	19% helix, 16% strand	P12737
N	Ribosomal protein L15E	protein	194	33% helix, 16% strand	—
O	Ribosomal protein L18	protein	186	39% helix, 13% strand	P14123
P	Ribosomal protein L18E	protein	115	46% helix, 23% strand	P12733
Q	Ribosomal protein L19E	protein	143	62% helix, 4% strand	P14119
R	Ribosomal protein L21E	protein	95	14% helix, 32% strand	P12734
S	Ribosomal protein L22	protein	150	29% helix, 31% strand	P10970
T	Ribosomal protein L23	protein	81	35% helix, 31% strand	P12732
U	Ribosomal protein L24	protein	119	29% helix, 29% strand	P10972
V	Ribosomal protein L24E	protein	53	19% helix, 19% strand	P14116
W	Ribosomal protein L29	protein	65	74% helix, 0% strand	P10971
X	Ribosomal protein L30	protein	154	38% helix, 14% strand	P14121
Y	Ribosomal protein L31E	protein	82	38% helix, 28% strand	P18138
Z	Ribosomal protein L32E	protein	142	23% helix, 12% strand	P12736
1	Ribosomal protein L37AE	protein	73	36% helix, 18% strand	—
2	Ribosomal protein L37E	protein	56	13% helix, 11% strand	P32410
3	Ribosomal protein L39E	protein	46	41% helix, 0% strand	P22452
4	Ribosomal protein L44E	protein	92	14% helix, 33% strand	P32411

Ligands and binding sites

SPR · Spiramycin I · ligand · chains A, E
MG · Magnesium ion · metal · 119 copies · chains A, C, E, D, S, T, X, B, 3, Z, Q, N, 4, L, U, 1
NA · Sodium ion · metal · 85 copies · chains A, M, D, 3, J, Z, S, U, B, K, E, N, 4, F, C, R, T
CD · Cadmium ion · metal · 5 copies · chains P, V, 1, 2, 4
K · Potassium ion · metal · 3 copies · chains A, N
CL · Chloride ion · ion · 22 copies · chains A, 3, L, M, K, Z, X, C, D, G, N, F, O, P, R, S, 4

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	1047	0.90	0.92	102	MG, NA
2	913	0.88	0.91	112	MG, CL
3	1074	0.86	0.88	102	empty
4	1175	0.86	0.89	106	MG
5	1119	0.86	0.88	103	NA

Interfaces

53 interfaces between chains.

A–D · 7354 Å² buried · 240 hydrogen bonds · protein-nucleic
A–N · 6868 Å² buried · 176 hydrogen bonds · protein-nucleic
A–C · 6265 Å² buried · 179 hydrogen bonds · protein-nucleic
A–E · 5608 Å² buried · 132 hydrogen bonds · protein-nucleic
A–Q · 4355 Å² buried · 121 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

1KD1 · Co-crystal Structure of Spiramycin bound to the 50S Ribosomal Subunit of Haloarcula… · the same entry in another collection · chain H against H, 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 P20276
Every structure of UniProt P20279
Every structure of UniProt P12735
Every structure of UniProt P14124
Every structure of UniProt P14135
Every structure of UniProt P12743
Every structure of UniProt P15825
Every structure of UniProt P29198
Every structure of UniProt P22450
Every structure of UniProt P12737
Every structure of UniProt P14123
Every structure of UniProt P12733
Every structure of UniProt P14119
Every structure of UniProt P12734
Every structure of UniProt P10970
Every structure of UniProt P12732
Every structure of UniProt P10972
Every structure of UniProt P14116
Every structure of UniProt P10971
Every structure of UniProt P14121
Every structure of UniProt P18138
Every structure of UniProt P12736
Every structure of UniProt P32410
Every structure of UniProt P22452
Every structure of UniProt P32411
Elsewhere: RCSB PDB 1KD1 · PDBe 1KD1 · UniProt P20276 · UniProt P20279 · UniProt P12735 · UniProt P14124 · UniProt P14135 · UniProt P12743 · UniProt P15825 · UniProt P29198 · UniProt P22450 · UniProt P12737 · UniProt P14123 · UniProt P12733 · UniProt P14119 · UniProt P12734 · UniProt P10970 · UniProt P12732 · UniProt P10972 · UniProt P14116 · UniProt P10971 · UniProt P14121 · UniProt P18138 · UniProt P12736 · UniProt P32410 · UniProt P22452 · UniProt P32411

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