MolNFT v1 · #138569 · protein

Structure of antibody 3D3 bound to the linear epitope of rsv G

5WNB · Mab 3D3 Fab heavy chain: “Structure of antibody 3D3 bound to the linear epitope of rsv G”. X-ray diffraction, 1 ligand (ZN), 11 pockets (best druggability 0.69). MolNFT v1 #138569 on GenesisL1: 3D structure, binding sites and…

PDB: 5WNB
Type: protein
Length: 877 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mab 3D3 Fab heavy chain; Mab 3D3 Fab light chain; Major surface glycoprotein G
UniProt: P03423
Ligands: ZN
Pockets: 11 · best druggability 0.69

Structure

x-ray diffraction · 5 distinct chains · 6% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Mab 3D3 Fab heavy chain	protein	226	5% helix, 51% strand	—
L	Mab 3D3 Fab light chain	protein	213	6% helix, 51% strand	—
I	Mab 3D3 Fab heavy chain	protein	216	6% helix, 53% strand	—
M	Mab 3D3 Fab light chain	protein	200	4% helix, 50% strand	—
A, B	Major surface glycoprotein G	protein	11	36% helix, 0% strand	P03423

Ligands and binding sites

ZN · Zinc ion · metal · 14 copies · chains H, L, B, M, I, A
ACY · Acetic acid · additive · 2 copies · chains L, B, M, A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	502	0.69	0.79	69	ZN
2	392	0.57	0.74	49	empty
3	317	0.56	0.76	48	empty
4	74	0.55	0.87	23	empty
5	216	0.52	0.77	32	empty

Interfaces

9 interfaces between chains.

H–L · 2061 Å² buried · 19 hydrogen bonds · protein-protein
I–M · 1711 Å² buried · 17 hydrogen bonds · protein-protein
H–B · 514 Å² buried · 4 hydrogen bonds · protein-protein
I–A · 485 Å² buried · 2 hydrogen bonds · protein-protein
H–I · 348 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

5WNB · Structure of antibody 3D3 bound to the linear epitope of RSV G · 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 P03423
Elsewhere: RCSB PDB 5WNB · PDBe 5WNB · UniProt P03423

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