MolNFT v2 · #226927 · protein

MAGE-A3 MHD crystal soaked with KL861

9BD2 · Melanoma-associated antigen 3: “MAGE-A3 MHD crystal soaked with KL861”. X-ray diffraction at 2.24, 1 ligand (A1AL3), 7 pockets (best druggability 0.76). MolNFT v2 #226927 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 9BD2
Type: protein
Length: 627 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.24
Source: Homo sapiens
Molecule: Melanoma-associated antigen 3
UniProt: P43357
Ligands: A1AL3
Pockets: 7 · best druggability 0.76

Structure

x-ray diffraction · resolution 2.24 · 1 distinct chain · 51% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Melanoma-associated antigen 3	protein	209	51% helix, 13% strand	P43357

Ligands and binding sites

A1AL3 · (furan-2-yl)[4-({(5P)-5-(1H-indazol-4-yl)-2-[3-(morpholin-4-yl)propoxy]phenyl}methyl)piperazin-1-yl]methanone · ligand · chains C

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

Pockets

7 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	77	0.76	0.98	25	empty
2	335	0.52	0.73	40	empty
3	211	0.50	0.75	33	empty
4	144	0.39	0.73	20	empty
5	78	0.35	0.75	16	empty

Interfaces

3 interfaces between chains.

B–C · 1489 Å² buried · 28 hydrogen bonds · protein-protein
A–C · 379 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 84 Å² buried · 0 hydrogen bonds · protein-protein

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 P43357
Elsewhere: RCSB PDB 9BD2 · PDBe 9BD2 · UniProt P43357

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