MolNFT v1 · #86905 · protein

Von hippel lindau PROTEIN:ELONGINB:ELONGINC complex, in complex with (2S,4R)-1-ethanoyl-N-[[4-(1,3-oxazol-5-YL)PHENYL]METHYL]-4-oxidanyl- pyrrolidine-2-carboxamide

4BKS · Transcription elongation factor B polypeptide 2: “Von hippel lindau PROTEIN:ELONGINB:ELONGINC complex, in complex with…”. X-ray diffraction, 1 ligand (X6C), 8 pockets (best druggability 0.59). MolNFT v1 #86905 on GenesisL1: 3D…

PDB: 4BKS
Type: protein
Length: 1,326 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: X6C
Pockets: 8 · best druggability 0.59

Structure

x-ray diffraction · 8 distinct chains · 29% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G, J	Transcription elongation factor B polypeptide 2	protein	103	15% helix, 37% strand	Q15370
B, E	Transcription elongation factor B polypeptide 1	protein	87	48% helix, 15% strand	Q15369
C	Von hippel-lindau disease tumor suppressor	protein	138	22% helix, 30% strand	P40337
D	Transcription elongation factor B polypeptide 2	protein	102	15% helix, 35% strand	Q15370
F	Von hippel-lindau disease tumor suppressor	protein	142	27% helix, 30% strand	P40337
H	Transcription elongation factor B polypeptide 1	protein	87	48% helix, 15% strand	Q15369
I, L	Von hippel-lindau disease tumor suppressor	protein	144	26% helix, 29% strand	P40337
K	Transcription elongation factor B polypeptide 1	protein	86	48% helix, 15% strand	Q15369

Ligands and binding sites

X6C · (2S,4R)-1-ethanoyl-N-[[4-(1,3-oxazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide · ligand · 4 copies · chains C, F, I, L
ACT · Acetate ion · additive · 2 copies · chains B, C, K, L

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	263	0.59	0.78	32	X6C
2	261	0.57	0.77	31	X6C
3	66	0.49	0.84	16	empty
4	158	0.42	0.74	24	empty
5	130	0.41	0.75	24	empty

Interfaces

16 interfaces between chains.

J–K · 1159 Å² buried · 14 hydrogen bonds · protein-protein
G–H · 1155 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1143 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 1083 Å² buried · 13 hydrogen bonds · protein-protein
K–L · 1077 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified (artifact).

Compared structures

4BKS · von Hippel Lindau protein:ElonginB:ElonginC complex, in complex with… · 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 4BKS · PDBe 4BKS · UniProt Q15370 · UniProt Q15369 · UniProt P40337

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