MolNFT v1 · #91258 · protein

The 6S snrnp assembly intermediate

4F7U · Small nuclear ribonucleoprotein sm D1: “The 6S snrnp assembly intermediate”. X-ray diffraction, 14 pockets (best druggability 0.74). MolNFT v1 #91258 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4F7U
Type: protein
Length: 1,002 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Small nuclear ribonucleoprotein sm D1; Small nuclear ribonucleoprotein sm D2; Small…
UniProt: P62315, P62317, P62305, P62321, P62309, A1ZAW5
Pockets: 14 · best druggability 0.74

Structure

x-ray diffraction · 12 distinct chains · 17% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Small nuclear ribonucleoprotein sm D1	protein	82	13% helix, 45% strand	P62315
B	Small nuclear ribonucleoprotein sm D2	protein	80	23% helix, 53% strand	P62317
C	Small nuclear ribonucleoprotein sm D1	protein	81	15% helix, 46% strand	P62315
D	Small nuclear ribonucleoprotein sm D2	protein	85	29% helix, 52% strand	P62317
E	Small nuclear ribonucleoprotein E	protein	78	18% helix, 54% strand	P62305
H	Small nuclear ribonucleoprotein E	protein	78	18% helix, 54% strand	P62305
F	Small nuclear ribonucleoprotein F	protein	73	15% helix, 58% strand	P62321
I	Small nuclear ribonucleoprotein F	protein	74	14% helix, 57% strand	P62321
G	Small nuclear ribonucleoprotein G	protein	68	16% helix, 59% strand	P62309
J	Small nuclear ribonucleoprotein G	protein	67	9% helix, 63% strand	P62309
Q	Methylosome subunit picln	protein	120	16% helix, 51% strand	A1ZAW5
P	Methylosome subunit picln	protein	116	16% helix, 52% strand	A1ZAW5

Ligands and binding sites

P6G · Hexaethylene glycol · additive · chains H, I

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	937	0.74	0.78	88	empty
2	843	0.69	0.75	66	empty
3	232	0.64	0.83	37	empty
4	511	0.64	0.77	42	empty
5	201	0.58	0.80	31	empty

Interfaces

16 interfaces between chains.

A–B · 1116 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 1083 Å² buried · 16 hydrogen bonds · protein-protein
E–G · 1013 Å² buried · 11 hydrogen bonds · protein-protein
H–J · 999 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 905 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

4F7U · The 6S snRNP assembly intermediate · the same entry in another collection · chain P against P, 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 P62315
Every structure of UniProt P62317
Every structure of UniProt P62305
Every structure of UniProt P62321
Every structure of UniProt P62309
Every structure of UniProt A1ZAW5
Elsewhere: RCSB PDB 4F7U · PDBe 4F7U · UniProt P62315 · UniProt P62317 · UniProt P62305 · UniProt P62321 · UniProt P62309 · UniProt A1ZAW5

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