MolNFT v1 · #100834 · protein

Crystal structure of the vif-cbfbeta-CUL5-elob-eloc pentameric complex

4N9F · Cullin-5: “Crystal structure of the vif-cbfbeta-CUL5-elob-eloc pentameric complex”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.81). MolNFT v1 #100834 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4N9F
Type: protein
Length: 9,494 residues
Chains: 60
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cullin-5; Transcription elongation factor B polypeptide 1; Transcription elongation…
UniProt: Q93034, Q15369, Q15370, Q13951, Q72499
Ligands: ZN
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 29 distinct chains · 51% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
U	Cullin-5	protein	299	79% helix, 0% strand	Q93034
Y, E, Q, Z, h, n, t, z, 5, T, B	Transcription elongation factor B polypeptide 1	protein	87	47% helix, 15% strand	Q15369
X, D, g, m, s, y, 4, H	Transcription elongation factor B polypeptide 2	protein	95	16% helix, 28% strand	Q15370
a	Core-binding factor subunit beta	protein	146	32% helix, 33% strand	Q13951
b	Virion infectivity factor	protein	172	31% helix, 25% strand	Q72499
C, l	Cullin-5	protein	297	78% helix, 0% strand	Q93034
F	Core-binding factor subunit beta	protein	145	32% helix, 33% strand	Q13951
G, S, d, v, 1, 7, 2	Virion infectivity factor	protein	170	32% helix, 23% strand	Q72499
I, V, f, r	Cullin-5	protein	296	80% helix, 0% strand	Q93034
K	Transcription elongation factor B polypeptide 1	protein	86	49% helix, 13% strand	Q15369
J	Transcription elongation factor B polypeptide 2	protein	90	16% helix, 29% strand	Q15370
L	Core-binding factor subunit beta	protein	144	31% helix, 34% strand	Q13951
M	Virion infectivity factor	protein	171	32% helix, 25% strand	Q72499
O	Cullin-5	protein	298	81% helix, 0% strand	Q93034
P	Transcription elongation factor B polypeptide 2	protein	94	15% helix, 34% strand	Q15370
R, 0	Core-binding factor subunit beta	protein	144	31% helix, 33% strand	Q13951
W	Transcription elongation factor B polypeptide 2	protein	91	18% helix, 29% strand	Q15370
c	Core-binding factor subunit beta	protein	145	33% helix, 33% strand	Q13951
i	Core-binding factor subunit beta	protein	155	33% helix, 32% strand	Q13951
j	Virion infectivity factor	protein	170	34% helix, 25% strand	Q72499
o, u	Core-binding factor subunit beta	protein	143	32% helix, 34% strand	Q13951
p, q	Virion infectivity factor	protein	169	33% helix, 25% strand	Q72499
x	Cullin-5	protein	294	81% helix, 0% strand	Q93034
3, 9	Cullin-5	protein	295	80% helix, 0% strand	Q93034
6	Core-binding factor subunit beta	protein	140	32% helix, 33% strand	Q13951
e	Transcription elongation factor B polypeptide 2	protein	79	19% helix, 35% strand	Q15370
k	Core-binding factor subunit beta	protein	147	34% helix, 33% strand	Q13951
w	Cullin-5	protein	296	79% helix, 0% strand	Q93034
N	Core-binding factor subunit beta	protein	145	32% helix, 31% strand	Q13951

Ligands and binding sites

ZN · Zinc ion · metal · 12 copies · chains b, G, M, S, c, d, j, o, p, v, 1, 7, k, q, 2

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	1089	0.81	0.83	93	empty
2	913	0.80	0.82	82	empty
3	688	0.80	0.84	71	empty
4	1107	0.78	0.80	87	empty
5	608	0.78	0.84	63	empty

Interfaces

135 interfaces between chains.

i–j · 2443 Å² buried · 28 hydrogen bonds · protein-protein
0–1 · 2369 Å² buried · 32 hydrogen bonds · protein-protein
6–7 · 2363 Å² buried · 29 hydrogen bonds · protein-protein
L–M · 2356 Å² buried · 29 hydrogen bonds · protein-protein
a–b · 2353 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

4N9F · Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex · the same entry in another collection · chain K against K, 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 Q93034
Every structure of UniProt Q15369
Every structure of UniProt Q15370
Every structure of UniProt Q13951
Every structure of UniProt Q72499
Elsewhere: RCSB PDB 4N9F · PDBe 4N9F · UniProt Q93034 · UniProt Q15369 · UniProt Q15370 · UniProt Q13951 · UniProt Q72499

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.