MolNFT v1 · #174105 · protein + RNA

50S-obge-gmppnp particle

7BL6 · 50S ribosomal protein L36: “50S-obge-gmppnp particle”. Electron microscopy, 3 ligands (GNP, ZN, MG), 20 pockets (best druggability 0.87). MolNFT v1 #174105 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7BL6
Type: protein + RNA
Length: 6,616 residues
Chains: 32
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 50S ribosomal protein L36; 50S ribosomal protein L2; 50S ribosomal protein L3; 50S…
EC: 3.6.5.-
UniProt: P0A7Q6, P60422, P60438, P60723, P62399, P0AG55, P0AA10, P02413, P0AG44, P0C018, P0A7L3, P0AG48, P61175, P0ADZ0, P60624, P68919, P0A7L8, P0A7M2, P0A7M6, P0AG51, P0A7N4, P0A7N9, P0A7P5, P0ADY3, P0A7K6, P0ADY7, P0A7R1, P0A7M9, P42641, P0A7Q1
Ligands: GNP, ZN, MG
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 32 distinct chains · 24% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
g	50S ribosomal protein L36	protein	38	8% helix, 34% strand	P0A7Q6
C	50S ribosomal protein L2	protein	271	6% helix, 27% strand	P60422
D	50S ribosomal protein L3	protein	209	9% helix, 36% strand	P60438
E	50S ribosomal protein L4	protein	193	37% helix, 12% strand	P60723
F	50S ribosomal protein L5	protein	177	37% helix, 18% strand	P62399
G	50S ribosomal protein L6	protein	176	20% helix, 35% strand	P0AG55
J	50S ribosomal protein L13	protein	142	34% helix, 21% strand	P0AA10
L	50S ribosomal protein L15	protein	144	15% helix, 8% strand	P02413
N	50S ribosomal protein L17	protein	120	45% helix, 15% strand	P0AG44
O	50S ribosomal protein L18	protein	116	41% helix, 16% strand	P0C018
Q	50S ribosomal protein L20	protein	117	78% helix, 0% strand	P0A7L3
R	50S ribosomal protein L21	protein	103	0% helix, 56% strand	P0AG48
S	50S ribosomal protein L22	protein	110	35% helix, 39% strand	P61175
T	50S ribosomal protein L23	protein	93	30% helix, 35% strand	P0ADZ0
U	50S ribosomal protein L24	protein	102	3% helix, 38% strand	P60624
V	50S ribosomal protein L25	protein	94	22% helix, 47% strand	P68919
W	50S ribosomal protein L27	protein	76	0% helix, 41% strand	P0A7L8
X	50S ribosomal protein L28	protein	77	26% helix, 31% strand	P0A7M2
Y	50S ribosomal protein L29	protein	63	60% helix, 0% strand	P0A7M6
Z	50S ribosomal protein L30	protein	58	33% helix, 26% strand	P0AG51
0	50S ribosomal protein L32	protein	56	20% helix, 9% strand	P0A7N4
1	50S ribosomal protein L33	protein	50	0% helix, 54% strand	P0A7N9
2	50S ribosomal protein L34	protein	46	57% helix, 0% strand	P0A7P5
K	50S ribosomal protein L14	protein	122	7% helix, 36% strand	P0ADY3
P	50S ribosomal protein L19	protein	113	13% helix, 42% strand	P0A7K6
M	50S ribosomal protein L16	protein	136	21% helix, 26% strand	P0ADY7
H	50S ribosomal protein L9	protein	149	34% helix, 19% strand	P0A7R1
d	50S ribosomal protein L31	protein	47	0% helix, 26% strand	P0A7M9
A	23S ribosomal RNA	rna	2897	—	—
B	5S ribosomal RNA	rna	119	—	—
9	GTPase OBGE/CGTA (EC 3.6.5.-)	protein	338	19% helix, 22% strand	P42641
3	50S ribosomal protein L35	protein	64	36% helix, 11% strand	P0A7Q1

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains 9
ZN · Zinc ion · metal · 2 copies · chains g, d
MG · Magnesium ion · metal · 2 copies · chains A, 9

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	1107	0.87	0.89	94	empty
2	852	0.87	0.90	88	empty
3	878	0.86	0.89	68	empty
4	1141	0.86	0.88	74	empty
5	546	0.86	0.92	65	empty

Interfaces

65 interfaces between chains.

C–A · 7339 Å² buried · 188 hydrogen bonds · protein-nucleic
D–A · 5056 Å² buried · 106 hydrogen bonds · protein-nucleic
L–A · 4462 Å² buried · 95 hydrogen bonds · protein-nucleic
Q–A · 4163 Å² buried · 91 hydrogen bonds · protein-nucleic
E–A · 3801 Å² buried · 77 hydrogen bonds · protein-nucleic

Compared structures

7BL6 · 50S-ObgE-GMPPNP particle · the same entry in another collection · chain Q against Q, 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 P0A7Q6
Every structure of UniProt P60422
Every structure of UniProt P60438
Every structure of UniProt P60723
Every structure of UniProt P62399
Every structure of UniProt P0AG55
Every structure of UniProt P0AA10
Every structure of UniProt P02413
Every structure of UniProt P0AG44
Every structure of UniProt P0C018
Every structure of UniProt P0A7L3
Every structure of UniProt P0AG48
Every structure of UniProt P61175
Every structure of UniProt P0ADZ0
Every structure of UniProt P60624
Every structure of UniProt P68919
Every structure of UniProt P0A7L8
Every structure of UniProt P0A7M2
Every structure of UniProt P0A7M6
Every structure of UniProt P0AG51
Every structure of UniProt P0A7N4
Every structure of UniProt P0A7N9
Every structure of UniProt P0A7P5
Every structure of UniProt P0ADY3
Every structure of UniProt P0A7K6
Every structure of UniProt P0ADY7
Every structure of UniProt P0A7R1
Every structure of UniProt P0A7M9
Every structure of UniProt P42641
Every structure of UniProt P0A7Q1
Elsewhere: RCSB PDB 7BL6 · PDBe 7BL6 · UniProt P0A7Q6 · UniProt P60422 · UniProt P60438 · UniProt P60723 · UniProt P62399 · UniProt P0AG55 · UniProt P0AA10 · UniProt P02413 · UniProt P0AG44 · UniProt P0C018 · UniProt P0A7L3 · UniProt P0AG48 · UniProt P61175 · UniProt P0ADZ0 · UniProt P60624 · UniProt P68919 · UniProt P0A7L8 · UniProt P0A7M2 · UniProt P0A7M6 · UniProt P0AG51 · UniProt P0A7N4 · UniProt P0A7N9 · UniProt P0A7P5 · UniProt P0ADY3 · UniProt P0A7K6 · UniProt P0ADY7 · UniProt P0A7R1 · UniProt P0A7M9 · UniProt P42641 · UniProt P0A7Q1

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