MolNFT v1 · #172722 · protein + RNA

Human pre-bact-2 spliceosome

7ABI · U5 small nuclear ribonucleoprotein 40 kda protein: “Human pre-bact-2 spliceosome”. Electron microscopy, 3 ligands (GTP, IHP, MG), 20 pockets (best druggability 0.87). MolNFT v1 #172722 on GenesisL1: 3D structure, binding sites and…

PDB: 7ABI
Type: protein + RNA
Length: 15,599 residues
Chains: 56
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: U5 small nuclear ribonucleoprotein 40 kda protein; Splicing factor 3B subunit 3; Small…
EC: 3.6.4.13, 5.2.1.8, 2.3.2.27
UniProt: Q96DI7, Q15393, P62306, P09661, Q15427, P62308, O60306, Q9BWJ5, P08579, Q9Y3B4, Q9BZL1, O75643, Q13573, Q9BRD0, Q8TAD8, P41223, Q9Y388, Q99459, Q96NC0, Q8WYA6, Q15029, Q9P013, Q8IYB3, O60870, Q9HCS7, P55081, Q9BZJ0, Q7RTV0, O43660, P62316, Q9UNP9, Q13356, P14678, P62318, Q6P2Q9, O60508, P62304, Q8NAV1, P62314, Q9NW64, Q15459, Q15428, Q12874, O75533, Q13435
Ligands: GTP, IHP, MG
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 56 distinct chains · 36% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D	U5 small nuclear ribonucleoprotein 40 kda protein	protein	302	0% helix, 49% strand	Q96DI7
E	Splicing factor 3B subunit 3	protein	1177	8% helix, 45% strand	Q15393
b	Small nuclear ribonucleoprotein F	protein	73	10% helix, 55% strand	P62306
W	U2 small nuclear ribonucleoprotein a'	protein	162	22% helix, 16% strand	P09661
w	Splicing factor 3B subunit 4	protein	78	26% helix, 23% strand	Q15427
d	Small nuclear ribonucleoprotein G	protein	69	10% helix, 43% strand	P62308
U	Intron-binding protein aquarius (EC 3.6.4.13)	protein	1329	48% helix, 12% strand	O60306
x	Splicing factor 3B subunit 5	protein	79	48% helix, 0% strand	Q9BWJ5
6	U6 snrna	rna	91	—	—
B	U2 small nuclear ribonucleoprotein B''	protein	169	27% helix, 30% strand	P08579
z	Splicing factor 3B subunit 6	protein	108	27% helix, 23% strand	Q9Y3B4
q	Ubiquitin-like protein 5	protein	73	22% helix, 27% strand	Q9BZL1
s	U5 small nuclear ribonucleoprotein 200 kda helicase (EC 3.6.4.13)	protein	1722	39% helix, 17% strand	O75643
v	Snw domain-containing protein 1	protein	206	36% helix, 4% strand	Q13573
3	BUD13 homolog	protein	55	40% helix, 0% strand	Q9BRD0
0	Smad nuclear-interacting protein 1	protein	150	5% helix, 17% strand	Q8TAD8
Q	Protein BUD31 homolog	protein	138	40% helix, 0% strand	P41223
1	RNA-binding motif protein, X-linked 2	protein	122	26% helix, 16% strand	Q9Y388
L	Cell division cycle 5-like protein	protein	116	54% helix, 0% strand	Q99459
N	Zinc finger matrin-type protein 2	protein	56	52% helix, 11% strand	Q96NC0
S	Beta-catenin-like protein 1	protein	355	76% helix, 0% strand	Q8WYA6
r	116 kda U5 small nuclear ribonucleoprotein component	protein	895	27% helix, 15% strand	Q15029
R	Spliceosome-associated protein CWC15 homolog	protein	44	20% helix, 2% strand	Q9P013
Y	SERINE/ARGININE repetitive matrix protein 1	protein	95	63% helix, 0% strand	Q8IYB3
7	DNA/RNA-binding protein KIN17	protein	236	37% helix, 29% strand	O60870
M	Pre-mRNA-splicing factor SYF1	protein	706	60% helix, 0% strand	Q9HCS7
K	Microfibrillar-associated protein 1	protein	123	34% helix, 0% strand	P55081
O	Crooked neck-like protein 1	protein	248	65% helix, 0% strand	Q9BZJ0
y	Phd finger-like domain-containing protein 5A	protein	100	8% helix, 29% strand	Q7RTV0
2	U2 snrna	rna	164	—	—
G	Pleiotropic regulator 1	protein	320	0% helix, 38% strand	O43660
h	Small nuclear ribonucleoprotein sm D2	protein	95	25% helix, 45% strand	P62316
o	Peptidyl-prolyl cis-trans isomerase E (EC 5.2.1.8)	protein	229	17% helix, 31% strand	Q9UNP9
i	Small nuclear ribonucleoprotein F	protein	72	13% helix, 60% strand	P62306
t	Ring-type E3 ubiquitin-protein ligase PPIL2 (EC 2.3.2.27)	protein	253	15% helix, 26% strand	Q13356
m	Small nuclear ribonucleoprotein-associated proteins B and B'	protein	82	4% helix, 55% strand	P14678
Z	Minx M3 pre-mRNA	rna	57	—	—
l	Small nuclear ribonucleoprotein sm D3	protein	83	19% helix, 42% strand	P62318
A	Pre-mRNA-processing-splicing factor 8	protein	2163	40% helix, 9% strand	Q6P2Q9
k	Small nuclear ribonucleoprotein G	protein	73	8% helix, 53% strand	P62308
8	Pre-mRNA-processing factor 17	protein	18	50% helix, 17% strand	O60508
j	Small nuclear ribonucleoprotein E	protein	81	16% helix, 56% strand	P62304
I	Pre-mRNA-splicing factor 38A	protein	176	49% helix, 7% strand	Q8NAV1
n	Small nuclear ribonucleoprotein sm D1	protein	80	6% helix, 45% strand	P62314
P	Pre-mRNA-splicing factor RBM22	protein	237	22% helix, 11% strand	Q9NW64
5	U5 snrna	rna	114	—	—
p	Splicing factor 3A subunit 1	protein	124	64% helix, 2% strand	Q15459
f	Small nuclear ribonucleoprotein-associated proteins B and B'	protein	64	0% helix, 52% strand	P14678
F	Splicing factor 3A subunit 2	protein	165	24% helix, 22% strand	Q15428
g	Small nuclear ribonucleoprotein sm D1	protein	93	22% helix, 41% strand	P62314
4	Splicing factor 3A subunit 3	protein	421	57% helix, 2% strand	Q12874
a	Small nuclear ribonucleoprotein sm D2	protein	78	14% helix, 42% strand	P62316
u	Splicing factor 3B subunit 1	protein	941	72% helix, 0% strand	O75533
e	Small nuclear ribonucleoprotein sm D3	protein	78	10% helix, 49% strand	P62318
T	Splicing factor 3B subunit 2	protein	183	31% helix, 2% strand	Q13435
c	Small nuclear ribonucleoprotein E	protein	78	8% helix, 46% strand	P62304

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · chains r
IHP · Inositol hexakisphosphate · ligand · chains Z, A
MG · Magnesium ion · metal · chains r

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	858	0.87	0.89	193	empty
2	979	0.86	0.87	135	empty
3	1010	0.86	0.87	154	empty
4	948	0.85	0.87	155	empty
5	1126	0.85	0.86	141	empty

Interfaces

144 interfaces between chains.

r–A · 1682 Å² buried · 9 hydrogen bonds · protein-protein
v–A · 1630 Å² buried · 7 hydrogen bonds · protein-protein
A–5 · 1303 Å² buried · 25 hydrogen bonds · protein-nucleic
6–2 · 1219 Å² buried · 93 hydrogen bonds · nucleic-nucleic
z–u · 1091 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

7ABI · Human pre-Bact-2 spliceosome · the same entry in another collection · chain z against z, TM-score 1.00

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