MolNFT v1 · #71301 · protein

Crystal structure of GP41 derived protein complexed with Fab 8066

3MA9 · Transmembrane glycoprotein: “Crystal structure of GP41 derived protein complexed with Fab 8066”. X-ray diffraction, 1 ligand (NA), 6 pockets (best druggability 0.54). MolNFT v1 #71301 on GenesisL1: 3D structure, binding sites and…

PDB: 3MA9
Type: protein
Length: 620 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transmembrane glycoprotein; FAB8066 Fab antibody fragment, heavy chain; FAB8066 Fab…
UniProt: D0VWW0
Ligands: NA
Pockets: 6 · best druggability 0.54

Structure

x-ray diffraction · 3 distinct chains · 35% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transmembrane glycoprotein	protein	197	91% helix, 0% strand	D0VWW0
H	FAB8066 Fab antibody fragment, heavy chain	protein	214	8% helix, 50% strand	—
L	FAB8066 Fab antibody fragment, light chain	protein	209	8% helix, 50% strand	—

Ligands and binding sites

NA · Sodium ion · metal · 2 copies · chains A, H, L

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	66	0.54	0.87	22	empty
2	157	0.41	0.74	22	empty
3	51	0.41	0.82	17	empty
4	58	0.31	0.76	17	empty
5	72	0.28	0.72	17	empty

Interfaces

3 interfaces between chains.

H–L · 1658 Å² buried · 16 hydrogen bonds · protein-protein
A–H · 866 Å² buried · 11 hydrogen bonds · protein-protein
A–L · 434 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

3MA9 · Crystal structure of gp41 derived protein complexed with fab 8066 · 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
Every structure of UniProt D0VWW0
Elsewhere: RCSB PDB 3MA9 · PDBe 3MA9 · UniProt D0VWW0

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