MolNFT v1 · #188373 · protein

Antibody DH1058 Fab fragment bound to SARS-cov-2 fusion peptide

7TOW · DH1058 Fab heavy chain: “Antibody DH1058 Fab fragment bound to SARS-cov-2 fusion peptide”. X-ray diffraction, 2 ligands (CA, PO4), 8 pockets (best druggability 0.72). MolNFT v1 #188373 on GenesisL1: 3D structure, binding sites and…

PDB: 7TOW
Type: protein
Length: 937 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DH1058 Fab heavy chain; DH1058 Fab light chain; Spike protein S2
UniProt: P0DTC2
Ligands: CA, PO4
Pockets: 8 · best druggability 0.72

Structure

x-ray diffraction · 5 distinct chains · 11% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	DH1058 Fab heavy chain	protein	236	9% helix, 48% strand	—
L, B	DH1058 Fab light chain	protein	214	6% helix, 50% strand	—
A	DH1058 Fab heavy chain	protein	235	8% helix, 48% strand	—
E	Spike protein S2	protein	15	60% helix, 0% strand	P0DTC2
D	Spike protein S2	protein	23	70% helix, 0% strand	P0DTC2

Ligands and binding sites

CA · Calcium ion · metal · 3 copies · chains H, E, L, A, B
PO4 · Phosphate ion · ion · 2 copies · chains H, L, A, B

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

Pockets

8 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	769	0.72	0.78	91	CA
2	1018	0.71	0.75	83	empty
3	358	0.64	0.79	45	empty
4	301	0.60	0.78	38	empty
5	68	0.48	0.84	22	empty

Interfaces

9 interfaces between chains.

H–L · 2156 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 2038 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 597 Å² buried · 8 hydrogen bonds · protein-protein
H–E · 537 Å² buried · 4 hydrogen bonds · protein-protein
H–A · 301 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

7TOW · Antibody DH1058 Fab fragment bound to SARS-CoV-2 fusion peptide · the same entry in another collection · chain H against H, 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 P0DTC2
Elsewhere: RCSB PDB 7TOW · PDBe 7TOW · UniProt P0DTC2

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