MolNFT v1 · #168888 · protein + RNA

50S subunit of 70S ribosome enterococcus faecalis multibody refinement

6WU9 · 23S rRNA: “50S subunit of 70S ribosome enterococcus faecalis multibody refinement”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.87). MolNFT v1 #168888 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6WU9
Type: protein + RNA
Length: 5,552 residues
Chains: 27
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 23S rRNA; 5S rRNA; 50S ribosomal protein L3; 50S ribosomal protein L4; 50S ribosomal…
UniProt: A0A1B4XKR3, A0A1B4XKU7, A0A1B4XKS2, A0A1B4XKU3, A0A1B4XSB2, A0A1B4XKS1, A0A1B4XKT1, A0A1B4XKU1, A0A1B4XKX1, A0A1B4XKS7, A0A1B4XPL8, A0A1B4XM76, A0A1B4XMC1, A0A1B4XKT6, A0A1B4XKR7, A0A1B4XKV5, A0A1B4XMB1, A0A1B4XRZ8, A0A1B4XKV0, A0A1B4XKW1, A0A1B4XMM2, A0A1B4XR98, A0A1B4XSI4, A0A1B4XM73, A0A1B4XKT9
Ligands: ZN
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 27 distinct chains · 24% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	23S rRNA	rna	2739	—	—
B	5S rRNA	rna	116	—	—
D	50S ribosomal protein L3	protein	207	8% helix, 43% strand	A0A1B4XKR3
E	50S ribosomal protein L4	protein	206	31% helix, 13% strand	A0A1B4XKU7
F	50S ribosomal protein L5	protein	177	32% helix, 12% strand	A0A1B4XKS2
G	50S ribosomal protein L6	protein	176	16% helix, 24% strand	A0A1B4XKU3
K	50S ribosomal protein L13	protein	145	31% helix, 19% strand	A0A1B4XSB2
L	50S ribosomal protein L14	protein	122	3% helix, 38% strand	A0A1B4XKS1
M	50S ribosomal protein L15	protein	146	16% helix, 9% strand	A0A1B4XKT1
N	50S ribosomal protein L16	protein	141	18% helix, 23% strand	A0A1B4XKU1
O	50S ribosomal protein L17	protein	124	41% helix, 15% strand	A0A1B4XKX1
P	50S ribosomal protein L18	protein	117	33% helix, 19% strand	A0A1B4XKS7
Q	50S ribosomal protein L19	protein	114	14% helix, 37% strand	A0A1B4XPL8
R	50S ribosomal protein L20	protein	118	75% helix, 0% strand	A0A1B4XM76
S	50S ribosomal protein L21	protein	102	0% helix, 55% strand	A0A1B4XMC1
T	50S ribosomal protein L22	protein	112	35% helix, 35% strand	A0A1B4XKT6
U	50S ribosomal protein L23	protein	89	20% helix, 37% strand	A0A1B4XKR7
V	50S ribosomal protein L24	protein	101	3% helix, 37% strand	A0A1B4XKV5
X	50S ribosomal protein L27	protein	76	0% helix, 42% strand	A0A1B4XMB1
Y	50S ribosomal protein L28	protein	54	7% helix, 48% strand	A0A1B4XRZ8
Z	50S ribosomal protein L29	protein	61	75% helix, 0% strand	A0A1B4XKV0
0	50S ribosomal protein L30	protein	58	40% helix, 28% strand	A0A1B4XKW1
2	50S ribosomal protein L32	protein	56	18% helix, 18% strand	A0A1B4XMM2
3	50S ribosomal protein L33	protein	49	0% helix, 59% strand	A0A1B4XR98
4	50S ribosomal protein L34	protein	44	55% helix, 0% strand	A0A1B4XSI4
5	50S ribosomal protein L35	protein	64	38% helix, 13% strand	A0A1B4XM73
6	50S ribosomal protein L36	protein	38	8% helix, 37% strand	A0A1B4XKT9

Ligands and binding sites

ZN · Zinc ion · metal · 3 copies · chains 2, 3, 6

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	839	0.87	0.91	61	empty
2	1159	0.87	0.89	98	empty
3	633	0.86	0.92	85	empty
4	674	0.85	0.91	66	empty
5	1041	0.85	0.87	74	empty

Interfaces

53 interfaces between chains.

A–D · 4938 Å² buried · 71 hydrogen bonds · protein-nucleic
A–M · 4315 Å² buried · 90 hydrogen bonds · protein-nucleic
A–E · 4302 Å² buried · 68 hydrogen bonds · protein-nucleic
A–R · 3903 Å² buried · 61 hydrogen bonds · protein-nucleic
A–O · 2893 Å² buried · 56 hydrogen bonds · protein-nucleic

Compared structures

6WU9 · 50S subunit of 70S Ribosome Enterococcus faecalis MultiBody refinement · the same entry in another collection · chain B against B, 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 A0A1B4XKR3
Every structure of UniProt A0A1B4XKU7
Every structure of UniProt A0A1B4XKS2
Every structure of UniProt A0A1B4XKU3
Every structure of UniProt A0A1B4XSB2
Every structure of UniProt A0A1B4XKS1
Every structure of UniProt A0A1B4XKT1
Every structure of UniProt A0A1B4XKU1
Every structure of UniProt A0A1B4XKX1
Every structure of UniProt A0A1B4XKS7
Every structure of UniProt A0A1B4XPL8
Every structure of UniProt A0A1B4XM76
Every structure of UniProt A0A1B4XMC1
Every structure of UniProt A0A1B4XKT6
Every structure of UniProt A0A1B4XKR7
Every structure of UniProt A0A1B4XKV5
Every structure of UniProt A0A1B4XMB1
Every structure of UniProt A0A1B4XRZ8
Every structure of UniProt A0A1B4XKV0
Every structure of UniProt A0A1B4XKW1
Every structure of UniProt A0A1B4XMM2
Every structure of UniProt A0A1B4XR98
Every structure of UniProt A0A1B4XSI4
Every structure of UniProt A0A1B4XM73
Every structure of UniProt A0A1B4XKT9
Elsewhere: RCSB PDB 6WU9 · PDBe 6WU9 · UniProt A0A1B4XKR3 · UniProt A0A1B4XKU7 · UniProt A0A1B4XKS2 · UniProt A0A1B4XKU3 · UniProt A0A1B4XSB2 · UniProt A0A1B4XKS1 · UniProt A0A1B4XKT1 · UniProt A0A1B4XKU1 · UniProt A0A1B4XKX1 · UniProt A0A1B4XKS7 · UniProt A0A1B4XPL8 · UniProt A0A1B4XM76 · UniProt A0A1B4XMC1 · UniProt A0A1B4XKT6 · UniProt A0A1B4XKR7 · UniProt A0A1B4XKV5 · UniProt A0A1B4XMB1 · UniProt A0A1B4XRZ8 · UniProt A0A1B4XKV0 · UniProt A0A1B4XKW1 · UniProt A0A1B4XMM2 · UniProt A0A1B4XR98 · UniProt A0A1B4XSI4 · UniProt A0A1B4XM73 · UniProt A0A1B4XKT9

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