MolNFT v1 · #148727 · protein + RNA

Human bact spliceosome core structure

6FF7 · RNA-binding motif protein, X-linked 2: “Human bact spliceosome core structure”. Electron microscopy, 5 ligands (ADP, IHP, GTP), 20 pockets (best druggability 0.86). MolNFT v1 #148727 on GenesisL1: 3D structure, binding sites and…

PDB: 6FF7
Type: protein + RNA
Length: 17,042 residues
Chains: 61
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA-binding motif protein, X-linked 2; U2 snrna; BUD13 homolog; U5 snrna; U6 snrna…
EC: 5.2.1.8, 2.3.2.27, 3.6.4.13
UniProt: Q9Y388, Q9BRD0, Q15428, Q13435, Q6P2Q9, Q15029, Q13573, O43660, O60508, Q99459, Q9BZJ0, Q9NW64, P41223, Q9P013, Q9UQ35, Q9Y3C6, Q8IYB3, Q6UX04, O15541, O75533, Q15393, Q9BWJ5, Q7RTV0, Q9Y3B4, Q8TAD8, Q12874, Q96DI7, Q9UMS4, O75934, Q9HCS7, Q9HCG8, O60306, P09661, P08579, P62316, P62306, P62304, P62308, P62318, P14678, P62314, Q9UNP9, Q15459, O60231, O75643, Q9ULR0
Ligands: ADP, IHP, GTP, ZN, MG
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 59 distinct chains · 36% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	RNA-binding motif protein, X-linked 2	protein	122	28% helix, 16% strand	Q9Y388
2	U2 snrna	rna	60	—	—
3	BUD13 homolog	protein	118	41% helix, 1% strand	Q9BRD0
5	U5 snrna	rna	70	—	—
6	U6 snrna	rna	95	—	—
7	Splicing factor 3A subunit 2	protein	93	37% helix, 10% strand	Q15428
8	Splicing factor 3B subunit 2	protein	144	34% helix, 0% strand	Q13435
A	Pre-mRNA-processing-splicing factor 8	protein	2238	37% helix, 10% strand	Q6P2Q9
B	116 kda U5 small nuclear ribonucleoprotein component	protein	902	28% helix, 15% strand	Q15029
C	Snw domain-containing protein 1	protein	286	30% helix, 5% strand	Q13573
D	Pleiotropic regulator 1	protein	320	0% helix, 42% strand	O43660
E	Pre-mRNA-processing factor 17	protein	130	24% helix, 9% strand	O60508
L	Cell division cycle 5-like protein	protein	103	50% helix, 0% strand	Q99459
O	Crooked neck-like protein 1	protein	253	62% helix, 1% strand	Q9BZJ0
P	Pre-mRNA-splicing factor RBM22	protein	286	21% helix, 8% strand	Q9NW64
Q	Protein BUD31 homolog	protein	138	37% helix, 0% strand	P41223
R	Spliceosome-associated protein CWC15 homolog	protein	102	24% helix, 0% strand	Q9P013
S	SERINE/ARGININE repetitive matrix protein 2	protein	34	0% helix, 3% strand	Q9UQ35
V	Peptidyl-prolyl cis-trans isomerase-like 1 (EC 5.2.1.8)	protein	159	15% helix, 25% strand	Q9Y3C6
Y	SERINE/ARGININE repetitive matrix protein 1	protein	95	63% helix, 0% strand	Q8IYB3
Z	Pre-mRNA	rna	48	—	—
s	Peptidyl-prolyl cis-trans isomerase CWC27 homolog (EC 5.2.1.8)	protein	175	11% helix, 26% strand	Q6UX04
t	Ring finger protein 113A	protein	172	20% helix, 5% strand	O15541
u	Splicing factor 3B subunit 1	protein	881	65% helix, 0% strand	O75533
v	Splicing factor 3B subunit 3	protein	1189	8% helix, 40% strand	Q15393
x	Splicing factor 3B subunit 5	protein	79	48% helix, 0% strand	Q9BWJ5
y	Phd finger-like domain-containing protein 5A	protein	100	12% helix, 23% strand	Q7RTV0
z, N	Splicing factor 3B subunit 6	protein	101	14% helix, 69% strand	Q9Y3B4
0	Smad nuclear-interacting protein 1	protein	155	6% helix, 34% strand	Q8TAD8
9	Splicing factor 3A subunit 3	protein	432	57% helix, 4% strand	Q12874
F	U5 small nuclear ribonucleoprotein 40 kda protein	protein	299	0% helix, 50% strand	Q96DI7
G	Pre-mRNA-processing factor 19 (EC 2.3.2.27)	protein	132	55% helix, 5% strand	Q9UMS4
H, J	Pre-mRNA-processing factor 19 (EC 2.3.2.27)	protein	135	53% helix, 1% strand	Q9UMS4
I	Pre-mRNA-processing factor 19 (EC 2.3.2.27)	protein	134	55% helix, 3% strand	Q9UMS4
K	Pre-mRNA-splicing factor SPF27	protein	213	66% helix, 0% strand	O75934
M	Pre-mRNA-splicing factor SYF1	protein	738	60% helix, 0% strand	Q9HCS7
T	Pre-mRNA-splicing factor CWC22 homolog	protein	462	65% helix, 2% strand	Q9HCG8
U	Intron-binding protein aquarius	protein	1329	49% helix, 12% strand	O60306
W	U2 small nuclear ribonucleoprotein a'	protein	162	25% helix, 19% strand	P09661
X	U2 small nuclear ribonucleoprotein B''	protein	171	29% helix, 22% strand	P08579
a	Small nuclear ribonucleoprotein sm D2	protein	89	16% helix, 45% strand	P62316
b	Small nuclear ribonucleoprotein F	protein	73	10% helix, 58% strand	P62306
c	Small nuclear ribonucleoprotein E	protein	78	9% helix, 47% strand	P62304
d	Small nuclear ribonucleoprotein G	protein	73	11% helix, 58% strand	P62308
e	Small nuclear ribonucleoprotein sm D3	protein	88	18% helix, 45% strand	P62318
f	Small nuclear ribonucleoprotein-associated proteins B and B'	protein	89	7% helix, 42% strand	P14678
g	Small nuclear ribonucleoprotein sm D1	protein	93	18% helix, 40% strand	P62314
h	Small nuclear ribonucleoprotein sm D2	protein	98	19% helix, 46% strand	P62316
i	Small nuclear ribonucleoprotein F	protein	74	15% helix, 57% strand	P62306
j	Small nuclear ribonucleoprotein E	protein	79	18% helix, 58% strand	P62304
k	Small nuclear ribonucleoprotein G	protein	74	8% helix, 54% strand	P62308
l	Small nuclear ribonucleoprotein sm D3	protein	83	13% helix, 46% strand	P62318
m	Small nuclear ribonucleoprotein-associated proteins B and B'	protein	71	10% helix, 56% strand	P14678
n	Small nuclear ribonucleoprotein sm D1	protein	82	16% helix, 45% strand	P62314
o	Peptidyl-prolyl cis-trans isomerase E (EC 5.2.1.8)	protein	229	17% helix, 31% strand	Q9UNP9
p	Splicing factor 3A subunit 1	protein	175	75% helix, 1% strand	Q15459
q	Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 (EC 3.6.4.13)	protein	625	43% helix, 19% strand	O60231
r	U5 small nuclear ribonucleoprotein 200 kda helicase (EC 3.6.4.13)	protein	1722	41% helix, 18% strand	O75643
w	Pre-mRNA-splicing factor ISY1 homolog	protein	56	89% helix, 0% strand	Q9ULR0

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains r
IHP · Inositol hexakisphosphate · ligand · chains A
GTP · Guanosine-5'-triphosphate · ligand · chains B
ZN · Zinc ion · metal · 11 copies · chains 2, 9, P, Q, Z, t, y
MG · Magnesium ion · metal · 5 copies · chains 6, Z

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	997	0.86	0.87	166	empty
2	1115	0.85	0.86	182	empty
3	936	0.85	0.86	159	empty
4	1061	0.84	0.85	148	empty
5	800	0.83	0.86	152	empty

Interfaces

154 interfaces between chains.

z–N · 3517 Å² buried · 603 hydrogen bonds · protein-protein
A–B · 1704 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 1624 Å² buried · 3 hydrogen bonds · protein-protein
2–6 · 1576 Å² buried · 105 hydrogen bonds · nucleic-nucleic
M–U · 1510 Å² buried · 40 hydrogen bonds · protein-protein

Compared structures

6FF7 · human Bact spliceosome core structure · the same entry in another collection · chain B against B, TM-score 1.00

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