MolNFT v1 · #148724 · protein + RNA

Human bact spliceosome core structure

6FF4 · RNA-binding motif protein, X-linked 2: “Human bact spliceosome core structure”. Electron microscopy, 4 ligands (IHP, GTP, ZN), 20 pockets (best druggability 0.88). MolNFT v1 #148724 on GenesisL1: 3D structure, binding sites and…

PDB: 6FF4
Type: protein + RNA
Length: 8,493 residues
Chains: 28
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
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
Ligands: IHP, GTP, ZN, MG
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 28 distinct chains · 32% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	RNA-binding motif protein, X-linked 2	protein	122	30% helix, 16% strand	Q9Y388
2	U2 snrna	rna	60	—	—
3	BUD13 homolog	protein	118	42% helix, 0% strand	Q9BRD0
5	U5 snrna	rna	70	—	—
6	U6 snrna	rna	95	—	—
7	Splicing factor 3A subunit 2	protein	93	38% helix, 10% strand	Q15428
8	Splicing factor 3B subunit 2	protein	144	35% helix, 0% strand	Q13435
A	Pre-mRNA-processing-splicing factor 8	protein	2238	37% helix, 11% strand	Q6P2Q9
B	116 kda U5 small nuclear ribonucleoprotein component	protein	902	29% helix, 16% strand	Q15029
C	Snw domain-containing protein 1	protein	286	31% helix, 5% strand	Q13573
D	Pleiotropic regulator 1	protein	320	1% helix, 43% strand	O43660
E	Pre-mRNA-processing factor 17	protein	130	28% helix, 9% strand	O60508
L	Cell division cycle 5-like protein	protein	103	48% helix, 0% strand	Q99459
O	Crooked neck-like protein 1	protein	253	65% helix, 0% strand	Q9BZJ0
P	Pre-mRNA-splicing factor RBM22	protein	286	23% helix, 8% strand	Q9NW64
Q	Protein BUD31 homolog	protein	138	43% helix, 0% strand	P41223
R	Spliceosome-associated protein CWC15 homolog	protein	102	22% helix, 1% 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	14% helix, 26% strand	Q9Y3C6
Y	SERINE/ARGININE repetitive matrix protein 1	protein	95	60% 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, 25% strand	Q6UX04
t	Ring finger protein 113A	protein	172	23% helix, 5% strand	O15541
u	Splicing factor 3B subunit 1	protein	881	66% 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	7% helix, 24% strand	Q7RTV0
z	Splicing factor 3B subunit 6	protein	101	16% helix, 20% strand	Q9Y3B4

Ligands and binding sites

IHP · Inositol hexakisphosphate · ligand · chains A, t
GTP · Guanosine-5'-triphosphate · ligand · chains A, B
ZN · Zinc ion · metal · 10 copies · chains P, Q, t, y
MG · Magnesium ion · metal · 4 copies · chains 6, 7

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	1110	0.88	0.89	110	empty
2	1153	0.88	0.89	100	empty
3	638	0.87	0.93	96	empty
4	644	0.86	0.91	73	MG
5	1061	0.84	0.85	99	empty

Interfaces

104 interfaces between chains.

A–B · 6173 Å² buried · 66 hydrogen bonds · protein-protein
A–C · 5151 Å² buried · 38 hydrogen bonds · protein-protein
A–t · 3604 Å² buried · 37 hydrogen bonds · protein-protein
8–u · 3231 Å² buried · 23 hydrogen bonds · protein-protein
5–A · 3129 Å² buried · 72 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

6FF4 · human Bact spliceosome core structure · the same entry in another collection · chain 7 against 7, 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 Q9Y388
Every structure of UniProt Q9BRD0
Every structure of UniProt Q15428
Every structure of UniProt Q13435
Every structure of UniProt Q6P2Q9
Every structure of UniProt Q15029
Every structure of UniProt Q13573
Every structure of UniProt O43660
Every structure of UniProt O60508
Every structure of UniProt Q99459
Every structure of UniProt Q9BZJ0
Every structure of UniProt Q9NW64
Every structure of UniProt P41223
Every structure of UniProt Q9P013
Every structure of UniProt Q9UQ35
Every structure of UniProt Q9Y3C6
Every structure of UniProt Q8IYB3
Every structure of UniProt Q6UX04
Every structure of UniProt O15541
Every structure of UniProt O75533
Every structure of UniProt Q15393
Every structure of UniProt Q9BWJ5
Every structure of UniProt Q7RTV0
Every structure of UniProt Q9Y3B4
Elsewhere: RCSB PDB 6FF4 · PDBe 6FF4 · UniProt Q9Y388 · UniProt Q9BRD0 · UniProt Q15428 · UniProt Q13435 · UniProt Q6P2Q9 · UniProt Q15029 · UniProt Q13573 · UniProt O43660 · UniProt O60508 · UniProt Q99459 · UniProt Q9BZJ0 · UniProt Q9NW64 · UniProt P41223 · UniProt Q9P013 · UniProt Q9UQ35 · UniProt Q9Y3C6 · UniProt Q8IYB3 · UniProt Q6UX04 · UniProt O15541 · UniProt O75533 · UniProt Q15393 · UniProt Q9BWJ5 · UniProt Q7RTV0 · UniProt Q9Y3B4

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