MolNFT v1 · #126750 · protein

Crystal structure of the heterotrimeric integrin-binding region of laminin-111

5MC9 · Laminin subunit alpha-1: “Crystal structure of the heterotrimeric integrin-binding region of laminin-111”. X-ray diffraction, 1 ligand (CA), 6 pockets (best druggability 0.77). MolNFT v1 #126750 on GenesisL1: 3D structure, binding…

PDB: 5MC9
Type: protein
Length: 701 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Laminin subunit alpha-1; Laminin subunit beta-1; Laminin subunit gamma-1
UniProt: P19137, P02469, P02468
Ligands: CA
Pockets: 6 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 18% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Laminin subunit alpha-1	protein	597	7% helix, 44% strand	P19137
B	Laminin subunit beta-1	protein	51	90% helix, 0% strand	P02469
C	Laminin subunit gamma-1	protein	53	74% helix, 2% strand	P02468

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1150	0.77	0.79	109	empty
2	292	0.68	0.83	45	empty
3	229	0.54	0.77	39	empty
4	72	0.38	0.78	13	empty
5	66	0.37	0.78	17	empty

Interfaces

3 interfaces between chains.

A–C · 1276 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1067 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 998 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5MC9 · Crystal structure of the heterotrimeric integrin-binding region of laminin-111 · the same entry in another collection · chain A against A, TM-score 1.00
P02468 · AlphaFold monomer V2.0 prediction for laminin subunit gamma-1 (P02468) · a predicted model of the same protein · chain C against A, TM-score 0.78
P02469 · AlphaFold monomer V2.0 prediction for laminin subunit beta-1 (P02469) · a predicted model of the same protein · chain B against A, TM-score 0.77

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 P19137
Every structure of UniProt P02469
Every structure of UniProt P02468
Elsewhere: RCSB PDB 5MC9 · PDBe 5MC9 · UniProt P19137 · UniProt P02469 · UniProt P02468

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