MolNFT v1 · #93222 · protein

Cqfd meditope

4GW1 · Fab light chain: “Cqfd meditope”. X-ray diffraction, 1 ligand (PO4), 7 pockets (best druggability 0.74). MolNFT v1 #93222 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4GW1
Type: protein
Length: 890 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab light chain; Fab heavy chain; Cqfd meditope
Ligands: PO4
Pockets: 7 · best druggability 0.74

Structure

x-ray diffraction · 5 distinct chains · 8% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fab light chain	protein	212	7% helix, 51% strand	—
B	Fab heavy chain	protein	221	10% helix, 52% strand	—
C	Fab light chain	protein	213	6% helix, 51% strand	—
D	Fab heavy chain	protein	220	8% helix, 52% strand	—
E, F	Cqfd meditope	protein	12	0% helix, 33% strand	—

Ligands and binding sites

PO4 · Phosphate ion · ion · 3 copies · chains A, 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1168	0.74	0.77	128	empty
2	405	0.63	0.78	50	empty
3	402	0.62	0.77	46	empty
4	296	0.54	0.75	58	empty
5	139	0.48	0.78	24	empty

Interfaces

8 interfaces between chains.

C–D · 1903 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1828 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 812 Å² buried · 12 hydrogen bonds · protein-protein
C–F · 518 Å² buried · 9 hydrogen bonds · protein-protein
A–E · 500 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

4GW1 · cQFD Meditope · 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 4GW1 · PDBe 4GW1

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