MolNFT v1 · #114393 · protein

Structure of SOCS2:ELONGIN C:ELONGIN B from dmso-treated crystals

5BO4 · Suppressor of cytokine signaling 2: “Structure of SOCS2:ELONGIN C:ELONGIN B from dmso-treated crystals”. X-ray diffraction, 19 pockets (best druggability 0.68). MolNFT v1 #114393 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5BO4
Type: protein
Length: 1,994 residues
Chains: 18
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Suppressor of cytokine signaling 2; Transcription elongation factor B polypeptide 2…
UniProt: O14508, Q15370, Q15369
Pockets: 19 · best druggability 0.68

Structure

x-ray diffraction · 13 distinct chains · 33% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, G, J	Suppressor of cytokine signaling 2	protein	154	38% helix, 18% strand	O14508
B	Transcription elongation factor B polypeptide 2	protein	103	17% helix, 33% strand	Q15370
C	Transcription elongation factor B polypeptide 1	protein	85	45% helix, 15% strand	Q15369
E	Transcription elongation factor B polypeptide 2	protein	95	20% helix, 34% strand	Q15370
F	Transcription elongation factor B polypeptide 1	protein	79	49% helix, 16% strand	Q15369
H	Transcription elongation factor B polypeptide 2	protein	103	21% helix, 35% strand	Q15370
I	Transcription elongation factor B polypeptide 1	protein	88	41% helix, 15% strand	Q15369
K, Q	Transcription elongation factor B polypeptide 2	protein	102	19% helix, 35% strand	Q15370
L	Transcription elongation factor B polypeptide 1	protein	84	43% helix, 14% strand	Q15369
M, P	Suppressor of cytokine signaling 2	protein	153	37% helix, 18% strand	O14508
N	Transcription elongation factor B polypeptide 2	protein	72	13% helix, 24% strand	Q15370
O	Transcription elongation factor B polypeptide 1	protein	79	46% helix, 16% strand	Q15369
R	Transcription elongation factor B polypeptide 1	protein	80	49% helix, 16% strand	Q15369

Pockets

19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	376	0.68	0.81	43	empty
2	316	0.56	0.76	44	empty
3	207	0.55	0.78	27	empty
4	170	0.53	0.79	28	empty
5	179	0.52	0.78	28	empty

Interfaces

26 interfaces between chains.

H–I · 1152 Å² buried · 16 hydrogen bonds · protein-protein
K–L · 1135 Å² buried · 14 hydrogen bonds · protein-protein
Q–R · 1128 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 1082 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 1015 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 11 modified (artifact).

Compared structures

Q15370 · AlphaFold monomer V2.0 prediction for elongin-B (Q15370) · a predicted model of the same protein · chain B against A, TM-score 0.98
O14508 · AlphaFold monomer V2.0 prediction for suppressor of cytokine signaling 2 (O14508) · a predicted model of the same protein · chain A against A, TM-score 0.98
Q15369 · AlphaFold monomer V2.0 prediction for elongin-C (Q15369) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 O14508
Every structure of UniProt Q15370
Every structure of UniProt Q15369
Elsewhere: RCSB PDB 5BO4 · PDBe 5BO4 · UniProt O14508 · UniProt Q15370 · UniProt Q15369

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