MolNFT v1 · #58717 · protein + RNA

The HSP15 protein fitted into the low resolution cryo-EM MAP of the 50S.NC-TRNA.HSP15 complex

3BBX · 5S ribosomal RNA: “The HSP15 protein fitted into the low resolution cryo-EM MAP of the 50S.NC-TRNA.HSP15 complex”. Electron microscopy, 1 ligand (MG), 20 pockets (best druggability 0.88). MolNFT v1 #58717 on GenesisL1: 3D structure…

PDB: 3BBX
Type: protein + RNA
Length: 6,195 residues
Chains: 30
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5S ribosomal RNA; 23S ribosomal RNA; 50S ribosomal protein L25; 50S ribosomal protein L2…
UniProt: P68919, P60422, P60438, P60723, P62399, P02390, P0A7R1, P02410, P02411, P02413, P02414, P02416, P0C018, P0A7K6, P0A7L3, P02422, P61175, P02424, P60624, P0A7L8, P0A7M6, P02430, P0A7M9, P0A7N4, P0A7N9, P0A7P5, P0A7Q1, P0A7Q6
Ligands: MG
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 30 distinct chains · 15% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5S ribosomal RNA	rna	117	—	—
B	23S ribosomal RNA	rna	2841	—	—
V	50S ribosomal protein L25	protein	94	17% helix, 22% strand	P68919
C	50S ribosomal protein L2	protein	267	2% helix, 4% strand	P60422
D	50S ribosomal protein L3	protein	209	2% helix, 3% strand	P60438
E	50S ribosomal protein L4	protein	201	16% helix, 2% strand	P60723
F	50S ribosomal protein L5	protein	178	15% helix, 4% strand	P62399
G	50S ribosomal protein L6	protein	176	20% helix, 24% strand	P02390
H	50S ribosomal protein L9	protein	149	29% helix, 8% strand	P0A7R1
J	50S ribosomal protein L13	protein	140	19% helix, 1% strand	P02410
K	50S ribosomal protein L14	protein	121	2% helix, 21% strand	P02411
L	50S ribosomal protein L15	protein	144	3% helix, 0% strand	P02413
M	50S ribosomal protein L16	protein	136	12% helix, 10% strand	P02414
N	50S ribosomal protein L17	protein	127	35% helix, 0% strand	P02416
O	50S ribosomal protein L18	protein	117	26% helix, 0% strand	P0C018
P	50S ribosomal protein L19	protein	114	0% helix, 5% strand	P0A7K6
Q	50S ribosomal protein L20	protein	117	69% helix, 0% strand	P0A7L3
R	50S ribosomal protein L21	protein	103	0% helix, 2% strand	P02422
S	50S ribosomal protein L22	protein	110	23% helix, 7% strand	P61175
T	50S ribosomal protein L23	protein	99	12% helix, 0% strand	P02424
U	50S ribosomal protein L24	protein	102	0% helix, 4% strand	P60624
W	50S ribosomal protein L27	protein	84	0% helix, 0% strand	P0A7L8
X	50S ribosomal protein L29	protein	63	41% helix, 0% strand	P0A7M6
Y	50S ribosomal protein L30	protein	58	31% helix, 9% strand	P02430
Z	50S ribosomal protein L31	protein	70	6% helix, 6% strand	P0A7M9
0	50S ribosomal protein L32	protein	56	9% helix, 0% strand	P0A7N4
1	50S ribosomal protein L33	protein	54	0% helix, 7% strand	P0A7N9
2	50S ribosomal protein L34	protein	46	39% helix, 0% strand	P0A7P5
3	50S ribosomal protein L35	protein	64	17% helix, 3% strand	P0A7Q1
4	50S ribosomal protein L36	protein	38	0% helix, 0% strand	P0A7Q6

Ligands and binding sites

MG · Magnesium ion · metal · 110 copies · chains B, R, C, 3, T, L, E, D, S, Q, U, 2

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	1000	0.88	0.90	116	empty
2	1142	0.85	0.87	99	MG
3	824	0.85	0.88	98	empty
4	924	0.83	0.86	71	MG
5	1090	0.82	0.84	101	empty

Interfaces

55 interfaces between chains.

B–C · 4556 Å² buried · 220 hydrogen bonds · protein-nucleic
B–D · 4219 Å² buried · 363 hydrogen bonds · protein-nucleic
B–Q · 3629 Å² buried · 170 hydrogen bonds · protein-nucleic
B–E · 3298 Å² buried · 97 hydrogen bonds · protein-nucleic
B–N · 2568 Å² buried · 50 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 isopeptide (isopeptide).

Compared structures

3BBX · The Hsp15 protein fitted into the low resolution Cryo-EM map of the 50S.nc-tRNA.Hsp15… · the same entry in another collection · chain A against A, 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 P68919
Every structure of UniProt P60422
Every structure of UniProt P60438
Every structure of UniProt P60723
Every structure of UniProt P62399
Every structure of UniProt P02390
Every structure of UniProt P0A7R1
Every structure of UniProt P02410
Every structure of UniProt P02411
Every structure of UniProt P02413
Every structure of UniProt P02414
Every structure of UniProt P02416
Every structure of UniProt P0C018
Every structure of UniProt P0A7K6
Every structure of UniProt P0A7L3
Every structure of UniProt P02422
Every structure of UniProt P61175
Every structure of UniProt P02424
Every structure of UniProt P60624
Every structure of UniProt P0A7L8
Every structure of UniProt P0A7M6
Every structure of UniProt P02430
Every structure of UniProt P0A7M9
Every structure of UniProt P0A7N4
Every structure of UniProt P0A7N9
Every structure of UniProt P0A7P5
Every structure of UniProt P0A7Q1
Every structure of UniProt P0A7Q6
Elsewhere: RCSB PDB 3BBX · PDBe 3BBX · UniProt P68919 · UniProt P60422 · UniProt P60438 · UniProt P60723 · UniProt P62399 · UniProt P02390 · UniProt P0A7R1 · UniProt P02410 · UniProt P02411 · UniProt P02413 · UniProt P02414 · UniProt P02416 · UniProt P0C018 · UniProt P0A7K6 · UniProt P0A7L3 · UniProt P02422 · UniProt P61175 · UniProt P02424 · UniProt P60624 · UniProt P0A7L8 · UniProt P0A7M6 · UniProt P02430 · UniProt P0A7M9 · UniProt P0A7N4 · UniProt P0A7N9 · UniProt P0A7P5 · UniProt P0A7Q1 · UniProt P0A7Q6

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