MolNFT v1 · #65639 · protein

Human RAVER1 RRM1 domain in complex with human vinculin tail domain vt

3H2V: “Human RAVER1 RRM1 domain in complex with human vinculin tail domain vt”. X-ray diffraction, 8 pockets (best druggability 0.79). MolNFT v1 #65639 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3H2V
Type: protein
Length: 977 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vinculin; Raver-1
UniProt: B4DTM7, Q8IY67
Pockets: 8 · best druggability 0.79

Structure

x-ray diffraction · 6 distinct chains · 64% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vinculin	protein	174	71% helix, 2% strand	B4DTM7
B	Vinculin	protein	167	74% helix, 1% strand	B4DTM7
C	Vinculin	protein	167	74% helix, 1% strand	B4DTM7
D	Vinculin	protein	175	71% helix, 2% strand	B4DTM7
E, G	Raver-1	protein	74	24% helix, 31% strand	Q8IY67
F, H	Raver-1	protein	73	25% helix, 36% strand	Q8IY67

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	791	0.79	0.82	85	empty
2	740	0.74	0.80	60	empty
3	164	0.45	0.75	23	empty
4	167	0.45	0.75	24	empty
5	92	0.35	0.75	19	empty

Interfaces

10 interfaces between chains.

B–F · 685 Å² buried · 14 hydrogen bonds · protein-protein
C–G · 676 Å² buried · 13 hydrogen bonds · protein-protein
D–H · 663 Å² buried · 9 hydrogen bonds · protein-protein
A–E · 660 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 377 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

3H2V · Human raver1 RRM1 domain in complex with human vinculin tail domain Vt · the same entry in another collection · chain H against H, TM-score 1.00
Q8IY67 · AlphaFold monomer V2.0 prediction for ribonucleoprotein ptb-binding 1 (Q8IY67) · a predicted model of the same protein · chain F against A, TM-score 0.99

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 B4DTM7
Every structure of UniProt Q8IY67
Elsewhere: RCSB PDB 3H2V · PDBe 3H2V · UniProt B4DTM7 · UniProt Q8IY67

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