MolNFT v1 · #125890 · protein

Llama nanobody PORM_19

5LMJ: “Llama nanobody PORM_19”. X-ray diffraction, 1 ligand (PO4), 5 pockets (best druggability 0.63). MolNFT v1 #125890 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5LMJ
Type: protein
Length: 492 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nanobody
Ligands: PO4
Pockets: 5 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Nanobody	protein	123	5% helix, 54% strand	—

Ligands and binding sites

PO4 · Phosphate ion · ion · 11 copies · chains A, D, B, C

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

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	424	0.63	0.77	45	PO4
2	218	0.55	0.78	26	PO4
3	196	0.47	0.75	25	PO4
4	152	0.46	0.77	37	empty
5	55	0.25	0.73	17	empty

Interfaces

4 interfaces between chains.

B–D · 866 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 566 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 520 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 415 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5LMJ · Llama nanobody PorM_19 · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 5LMJ · PDBe 5LMJ

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.