MolNFT v1 · #172721 · protein + RNA

Human pre-bact-2 spliceosome (SF3B/U2 snrnp portion)

7ABH · Cell division cycle 5-like protein: “Human pre-bact-2 spliceosome (SF3B/U2 snrnp portion)”. Electron microscopy, 20 pockets (best druggability 0.86). MolNFT v1 #172721 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7ABH
Type: protein + RNA
Length: 3,353 residues
Chains: 16
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cell division cycle 5-like protein; Phd finger-like domain-containing protein 5A; Minx M3…
UniProt: Q99459, Q7RTV0, Q15428, Q12874, O75533, Q13435, Q15393, Q15427, Q9BWJ5, Q9Y3B4, Q8TAD8, Q9Y388, Q8IYB3, O60870
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 16 distinct chains · 35% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Cell division cycle 5-like protein	protein	48	58% helix, 0% strand	Q99459
y	Phd finger-like domain-containing protein 5A	protein	100	8% helix, 29% strand	Q7RTV0
Z	Minx M3 pre-mRNA	rna	28	—	—
F	Splicing factor 3A subunit 2	protein	75	51% helix, 12% strand	Q15428
4	Splicing factor 3A subunit 3	protein	108	40% helix, 6% strand	Q12874
u	Splicing factor 3B subunit 1	protein	932	72% helix, 0% strand	O75533
T	Splicing factor 3B subunit 2	protein	183	34% helix, 2% strand	Q13435
E	Splicing factor 3B subunit 3	protein	1177	7% helix, 43% strand	Q15393
w	Splicing factor 3B subunit 4	protein	78	26% helix, 27% strand	Q15427
x	Splicing factor 3B subunit 5	protein	79	46% helix, 0% strand	Q9BWJ5
z	Splicing factor 3B subunit 6	protein	108	27% helix, 19% strand	Q9Y3B4
0	Smad nuclear-interacting protein 1	protein	150	4% helix, 17% strand	Q8TAD8
1	RNA-binding motif protein, X-linked 2	protein	122	32% helix, 16% strand	Q9Y388
Y	SERINE/ARGININE repetitive matrix protein 1	protein	95	64% helix, 0% strand	Q8IYB3
2	U2 snrna	rna	37	—	—
7	DNA/RNA-binding protein KIN17	protein	33	94% helix, 0% strand	O60870

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	980	0.86	0.87	173	empty
2	880	0.80	0.83	98	empty
3	366	0.79	0.89	87	empty
4	304	0.78	0.90	58	empty
5	313	0.78	0.89	61	empty

Interfaces

36 interfaces between chains.

u–T · 968 Å² buried · 5 hydrogen bonds · protein-protein
u–z · 830 Å² buried · 3 hydrogen bonds · protein-protein
Z–u · 796 Å² buried · 6 hydrogen bonds · protein-nucleic
E–x · 653 Å² buried · 0 hydrogen bonds · protein-protein
Z–2 · 637 Å² buried · 45 hydrogen bonds · nucleic-nucleic

Compared structures

7ABH · Human pre-Bact-2 spliceosome (SF3b/U2 snRNP portion) · the same entry in another collection · chain z against z, 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 Q99459
Every structure of UniProt Q7RTV0
Every structure of UniProt Q15428
Every structure of UniProt Q12874
Every structure of UniProt O75533
Every structure of UniProt Q13435
Every structure of UniProt Q15393
Every structure of UniProt Q15427
Every structure of UniProt Q9BWJ5
Every structure of UniProt Q9Y3B4
Every structure of UniProt Q8TAD8
Every structure of UniProt Q9Y388
Every structure of UniProt Q8IYB3
Every structure of UniProt O60870
Elsewhere: RCSB PDB 7ABH · PDBe 7ABH · UniProt Q99459 · UniProt Q7RTV0 · UniProt Q15428 · UniProt Q12874 · UniProt O75533 · UniProt Q13435 · UniProt Q15393 · UniProt Q15427 · UniProt Q9BWJ5 · UniProt Q9Y3B4 · UniProt Q8TAD8 · UniProt Q9Y388 · UniProt Q8IYB3 · UniProt O60870

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