MolNFT v1 · #119797 · protein + RNA

Rnc in complex with srp-sr in the closed state

5GAG · Srp 4.5S RNA: “Rnc in complex with srp-sr in the closed state”. Electron microscopy, 2 ligands (MG, ZN), 20 pockets (best druggability 0.88). MolNFT v1 #119797 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5GAG
Type: protein + RNA
Length: 6,685 residues
Chains: 36
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Srp 4.5S RNA; TRNA ccaend; 23S rRNA; 5S rRNA; 50S ribosomal protein L2; 50S ribosomal…
UniProt: P60422, P60438, P60723, P62399, P0AG55, P0A7R1, P0A7J3, P0A7J7, P0AA10, P0ADY3, P02413, P0ADY7, P0AG44, P0C018, P0A7K6, P0A7L3, P0AG48, P61175, P0ADZ0, P60624, P68919, P0A7L8, P0A7M2, P0A7M6, P0AG51, P0A7N4, P0A7N9, P0A7P5, P0A7Q1, P0A7Q6
Ligands: MG, ZN
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 36 distinct chains · 28% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	Srp 4.5S RNA	rna	43	—	—
2	TRNA ccaend	rna	3	—	—
A	23S rRNA	rna	2883	—	—
B	5S rRNA	rna	120	—	—
C	50S ribosomal protein L2	protein	271	6% helix, 28% strand	P60422
D	50S ribosomal protein L3	protein	209	10% helix, 35% strand	P60438
E	50S ribosomal protein L4	protein	201	35% helix, 12% strand	P60723
F	50S ribosomal protein L5	protein	177	37% helix, 21% strand	P62399
G	50S ribosomal protein L6	protein	176	17% helix, 36% strand	P0AG55
H	50S ribosomal protein L9	protein	149	34% helix, 26% strand	P0A7R1
I	50S ribosomal protein L10	protein	125	34% helix, 18% strand	P0A7J3
J	50S ribosomal protein L11	protein	134	41% helix, 19% strand	P0A7J7
K	50S ribosomal protein L13	protein	142	32% helix, 19% strand	P0AA10
L	50S ribosomal protein L14	protein	123	7% helix, 38% strand	P0ADY3
M	50S ribosomal protein L15	protein	144	18% helix, 14% strand	P02413
N	50S ribosomal protein L16	protein	136	19% helix, 28% strand	P0ADY7
O	50S ribosomal protein L17	protein	125	54% helix, 16% strand	P0AG44
P	50S ribosomal protein L18	protein	117	44% helix, 20% strand	P0C018
Q	50S ribosomal protein L19	protein	114	16% helix, 45% strand	P0A7K6
R	50S ribosomal protein L20	protein	117	79% helix, 0% strand	P0A7L3
S	50S ribosomal protein L21	protein	103	0% helix, 64% strand	P0AG48
T	50S ribosomal protein L22	protein	110	41% helix, 36% strand	P61175
U	50S ribosomal protein L23	protein	95	26% helix, 37% strand	P0ADZ0
V	50S ribosomal protein L24	protein	102	3% helix, 51% strand	P60624
W	50S ribosomal protein L25	protein	94	21% helix, 48% strand	P68919
X	50S ribosomal protein L27	protein	76	0% helix, 41% strand	P0A7L8
Y	50S ribosomal protein L28	protein	77	27% helix, 36% strand	P0A7M2
Z	50S ribosomal protein L29	protein	62	74% helix, 0% strand	P0A7M6
a	50S ribosomal protein L30	protein	58	34% helix, 26% strand	P0AG51
b	50S ribosomal protein L32	protein	56	20% helix, 14% strand	P0A7N4
c	50S ribosomal protein L33	protein	51	0% helix, 57% strand	P0A7N9
d	50S ribosomal protein L34	protein	46	52% helix, 0% strand	P0A7P5
e	50S ribosomal protein L35	protein	64	31% helix, 11% strand	P0A7Q1
f	50S ribosomal protein L36	protein	38	8% helix, 47% strand	P0A7Q6
i	Signal recognition particle protein ffh	protein	126	57% helix, 0% strand	—
k	1A9L ss	protein	18	78% helix, 0% strand	—

Ligands and binding sites

MG · Magnesium ion · metal · 431 copies · chains 2, A, E, M, D, C, e, U, K, O, T, R, b, N, X, G, d, B, Y
ZN · Zinc ion · metal · chains f

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	1028	0.88	0.90	106	MG
2	1135	0.88	0.91	109	MG
3	1143	0.88	0.90	96	MG
4	858	0.86	0.89	89	MG
5	612	0.85	0.91	79	MG

Interfaces

70 interfaces between chains.

A–C · 7134 Å² buried · 183 hydrogen bonds · protein-nucleic
A–D · 5063 Å² buried · 105 hydrogen bonds · protein-nucleic
A–M · 4490 Å² buried · 113 hydrogen bonds · protein-nucleic
A–E · 4163 Å² buried · 86 hydrogen bonds · protein-nucleic
A–R · 4116 Å² buried · 101 hydrogen bonds · protein-nucleic

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 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 P0A7R1
Every structure of UniProt P0A7J3
Every structure of UniProt P0A7J7
Every structure of UniProt P0AA10
Every structure of UniProt P0ADY3
Every structure of UniProt P02413
Every structure of UniProt P0ADY7
Every structure of UniProt P0AG44
Every structure of UniProt P0C018
Every structure of UniProt P0A7K6
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 P0A7Q1
Every structure of UniProt P0A7Q6
Elsewhere: RCSB PDB 5GAG · PDBe 5GAG · UniProt P60422 · UniProt P60438 · UniProt P60723 · UniProt P62399 · UniProt P0AG55 · UniProt P0A7R1 · UniProt P0A7J3 · UniProt P0A7J7 · UniProt P0AA10 · UniProt P0ADY3 · UniProt P02413 · UniProt P0ADY7 · UniProt P0AG44 · UniProt P0C018 · UniProt P0A7K6 · 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 P0A7Q1 · UniProt P0A7Q6

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