MolNFT v1 · #108822 · protein

CCM2 ptb domain in complex with KRIT1 NPXY/F3

4WJ7 · Malcavernin: “CCM2 ptb domain in complex with KRIT1 NPXY/F3”. X-ray diffraction, 5 pockets (best druggability 0.70). MolNFT v1 #108822 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4WJ7
Type: protein
Length: 566 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Malcavernin; KRIT1 NPXY/F3
UniProt: Q9BSQ5
Pockets: 5 · best druggability 0.70

Structure

x-ray diffraction · 6 distinct chains · 24% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Malcavernin	protein	137	24% helix, 40% strand	Q9BSQ5
B	Malcavernin	protein	132	23% helix, 41% strand	Q9BSQ5
C	Malcavernin	protein	129	26% helix, 43% strand	Q9BSQ5
D	Malcavernin	protein	123	24% helix, 44% strand	Q9BSQ5
W, Y, Z	KRIT1 NPXY/F3	protein	11	0% helix, 36% strand	—
X	KRIT1 NPXY/F3	protein	12	0% helix, 33% strand	—

Pockets

5 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	498	0.70	0.80	67	empty
2	356	0.66	0.80	29	empty
3	193	0.46	0.75	32	empty
4	59	0.42	0.81	13	empty
5	54	0.30	0.76	13	empty

Interfaces

11 interfaces between chains.

B–X · 746 Å² buried · 10 hydrogen bonds · protein-protein
C–Y · 737 Å² buried · 11 hydrogen bonds · protein-protein
A–W · 673 Å² buried · 9 hydrogen bonds · protein-protein
D–Z · 644 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 556 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

4WJ7 · CCM2 PTB domain in complex with KRIT1 NPxY/F3 · the same entry in another collection · chain Z against Z, TM-score 1.00
Q9BSQ5 · AlphaFold monomer V2.0 prediction for cerebral cavernous malformations 2 protein (Q9BSQ5) · a predicted model of the same protein · chain C 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 Q9BSQ5
Elsewhere: RCSB PDB 4WJ7 · PDBe 4WJ7 · UniProt Q9BSQ5

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