MolNFT v1 · #125855 · protein

PVHL:ELOB:ELOC in complex with VH298

5LLI · Transcription elongation factor B polypeptide 2: “PVHL:ELOB:ELOC in complex with VH298”. X-ray diffraction, 1 ligand (6Z3), 8 pockets (best druggability 0.63). MolNFT v1 #125855 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5LLI
Type: protein
Length: 1,339 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcription elongation factor B polypeptide 2; Transcription elongation factor B…
UniProt: Q15370, Q15369, P40337
Ligands: 6Z3
Pockets: 8 · best druggability 0.63

Structure

x-ray diffraction · 8 distinct chains · 32% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transcription elongation factor B polypeptide 2	protein	104	17% helix, 38% strand	Q15370
B	Transcription elongation factor B polypeptide 1	protein	87	48% helix, 15% strand	Q15369
C	Von hippel-lindau disease tumor suppressor	protein	142	23% helix, 30% strand	P40337
D, G, J	Transcription elongation factor B polypeptide 2	protein	103	15% helix, 39% strand	Q15370
E	Transcription elongation factor B polypeptide 1	protein	91	46% helix, 14% strand	Q15369
F, I, L	Von hippel-lindau disease tumor suppressor	protein	143	27% helix, 29% strand	P40337
H	Transcription elongation factor B polypeptide 1	protein	89	46% helix, 15% strand	Q15369
K	Transcription elongation factor B polypeptide 1	protein	88	48% helix, 15% strand	Q15369

Ligands and binding sites

6Z3 · (2~{S},4~{R})-1-[(2~{S})-2-[(1-cyanocyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide · ligand · 4 copies · chains C, L, F, I

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	299	0.63	0.80	41	6Z3
2	293	0.62	0.79	42	6Z3
3	174	0.45	0.75	27	empty
4	151	0.44	0.75	28	empty
5	128	0.38	0.74	22	empty

Interfaces

18 interfaces between chains.

G–H · 1152 Å² buried · 11 hydrogen bonds · protein-protein
J–K · 1139 Å² buried · 13 hydrogen bonds · protein-protein
D–E · 1131 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 1126 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 1078 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (artifact).

Compared structures

5LLI · pVHL:EloB:EloC in complex with VH298 · the same entry in another collection · chain L against L, 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 Q15370
Every structure of UniProt Q15369
Every structure of UniProt P40337
Elsewhere: RCSB PDB 5LLI · PDBe 5LLI · UniProt Q15370 · UniProt Q15369 · UniProt P40337

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