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Crystal structure of merlin complexed with DCAF1/VPRBP

Analyse Crystal structure of merlin complexed with DCAF1/VPRBP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3WA0
Type: protein
Length: 1,793 residues
Chains: 11
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Merlin; Protein vprbp
UniProt: P46662, Q9Y4B6
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 11 distinct chains · 35% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Merlin	protein	289	36% helix, 22% strand	P46662
B	Merlin	protein	290	37% helix, 23% strand	P46662
C	Merlin	protein	293	37% helix, 24% strand	P46662
D	Merlin	protein	295	37% helix, 25% strand	P46662
E	Merlin	protein	292	36% helix, 23% strand	P46662
F	Merlin	protein	291	35% helix, 24% strand	P46662
G	Protein vprbp	protein	11	0% helix, 36% strand	Q9Y4B6
H	Protein vprbp	protein	11	0% helix, 36% strand	Q9Y4B6
I	Protein vprbp	protein	7	0% helix, 43% strand	—
J	Protein vprbp	protein	8	0% helix, 50% strand	—
K	Protein vprbp	protein	6	0% helix, 50% strand	—

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	807	0.80	0.83	81	empty
2	1085	0.79	0.80	90	empty
3	1060	0.78	0.80	98	empty
4	727	0.77	0.82	90	empty
5	390	0.62	0.77	36	empty

Interfaces

17 interfaces between chains.

A–D · 645 Å² buried · 13 hydrogen bonds · protein-protein
C–E · 603 Å² buried · 12 hydrogen bonds · protein-protein
B–H · 533 Å² buried · 11 hydrogen bonds · protein-protein
A–G · 517 Å² buried · 7 hydrogen bonds · protein-protein
C–F · 517 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

3WA0 · Crystal structure of merlin complexed with DCAF1/VprBP · the same entry in another collection · chain K against K, TM-score 1.00
P46662 · AlphaFold monomer V2.0 prediction for merlin (P46662) · a predicted model of the same protein · chain B 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 P46662
Every structure of UniProt Q9Y4B6
Elsewhere: RCSB PDB 3WA0 · PDBe 3WA0 · UniProt P46662 · UniProt Q9Y4B6

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