MolNFT v1 · #81360 · protein

Crystal structure of the MALT1 paracaspase (P21 form)

3UOA · Mucosa-associated lymphoid tissue lymphoma translocation…: “Crystal structure of the MALT1 paracaspase (P21 form)”. X-ray diffraction, 1 ligand (MG), 12 pockets (best druggability 0.79). MolNFT v1 #81360 on GenesisL1: 3D structure…

PDB: 3UOA
Type: protein
Length: 735 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mucosa-associated lymphoid tissue lymphoma translocation protein 1…
UniProt: Q9UDY8
Ligands: MG
Pockets: 12 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 22% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Mucosa-associated lymphoid tissue lymphoma translocation protein 1	protein	364	21% helix, 29% strand	Q9UDY8
C	Mucosa-associated lymphoid tissue lymphoma translocation protein 1	protein	363	22% helix, 29% strand	Q9UDY8
L, M	Z-val-arg-pro-dl-arg-fluoromethylketone	protein	4	0% helix, 50% strand	—

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains C

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

Pockets

12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	240	0.79	0.92	37	empty
2	260	0.79	0.91	36	empty
3	134	0.59	0.83	21	empty
4	69	0.51	0.85	22	empty
5	205	0.50	0.76	42	empty

Interfaces

3 interfaces between chains.

B–C · 1373 Å² buried · 12 hydrogen bonds · protein-protein
B–L · 549 Å² buried · 15 hydrogen bonds · protein-protein
C–M · 546 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

3UOA · Crystal structure of the MALT1 paracaspase (P21 form) · the same entry in another collection · chain B against B, TM-score 1.00
Q9UDY8 · AlphaFold monomer V2.0 prediction for mucosa-associated lymphoid tissue lymphoma… · 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 Q9UDY8
Elsewhere: RCSB PDB 3UOA · PDBe 3UOA · UniProt Q9UDY8

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