MolNFT v1 · #146257 · protein

Rsv prefusion F in complex with AM22 Fab

6DC5 · Rsv fusion glycoprotein: “Rsv prefusion F in complex with AM22 Fab”. X-ray diffraction, 2 ligands (NAG, CD), 20 pockets (best druggability 0.82). MolNFT v1 #146257 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6DC5
Type: protein
Length: 2,643 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rsv fusion glycoprotein; Fab AM22 heavy chain; Fab AM22 light chain
UniProt: P03420, M1E1E4, Q6GMX6, Q8TCD0
Ligands: NAG, CD
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 8 distinct chains · 20% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rsv fusion glycoprotein	protein	445	30% helix, 33% strand	P03420, M1E1E4
D	Rsv fusion glycoprotein	protein	449	30% helix, 33% strand	P03420, M1E1E4
G	Rsv fusion glycoprotein	protein	444	30% helix, 33% strand	P03420, M1E1E4
B, E	Fab AM22 heavy chain	protein	221	6% helix, 53% strand	Q6GMX6
C	Fab AM22 light chain	protein	213	7% helix, 53% strand	Q8TCD0
F	Fab AM22 light chain	protein	212	8% helix, 51% strand	Q8TCD0
H	Fab AM22 heavy chain	protein	223	7% helix, 52% strand	Q6GMX6
I	Fab AM22 light chain	protein	215	7% helix, 52% strand	Q8TCD0

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, D, E, G, H
CD · Cadmium ion · metal · 3 copies · chains A, D, G
PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains B, C, I, E, F, H

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1127	0.82	0.83	78	empty
2	729	0.80	0.84	60	empty
3	907	0.77	0.80	81	empty
4	840	0.76	0.80	80	empty
5	706	0.72	0.79	35	empty

Interfaces

15 interfaces between chains.

A–G · 2303 Å² buried · 27 hydrogen bonds · protein-protein
A–D · 2287 Å² buried · 19 hydrogen bonds · protein-protein
D–G · 2101 Å² buried · 21 hydrogen bonds · protein-protein
H–I · 1949 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 1836 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 37 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

6DC5 · RSV prefusion F in complex with AM22 Fab · the same entry in another collection · chain B against B, 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 P03420
Every structure of UniProt M1E1E4
Every structure of UniProt Q6GMX6
Every structure of UniProt Q8TCD0
Elsewhere: RCSB PDB 6DC5 · PDBe 6DC5 · UniProt P03420 · UniProt M1E1E4 · UniProt Q6GMX6 · UniProt Q8TCD0

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