MolNFT v1 · #135918 · protein

Crystal structure of rsv F B9320 bound to MEDI8897

5UDD · Fusion glycoprotein F0: “Crystal structure of rsv F B9320 bound to MEDI8897”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.83). MolNFT v1 #135918 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5UDD
Type: protein
Length: 6,648 residues
Chains: 21
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fusion glycoprotein F0; MEDI8897 Fab heavy chain; MEDI8897 Fab light chain
UniProt: Q6V2E7
Ligands: SO4
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 16 distinct chains · 24% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fusion glycoprotein F0	protein	449	31% helix, 33% strand	Q6V2E7
B	Fusion glycoprotein F0	protein	452	32% helix, 33% strand	Q6V2E7
C	Fusion glycoprotein F0	protein	450	32% helix, 34% strand	Q6V2E7
D	Fusion glycoprotein F0	protein	455	31% helix, 33% strand	Q6V2E7
E	Fusion glycoprotein F0	protein	451	32% helix, 33% strand	Q6V2E7
F	Fusion glycoprotein F0	protein	452	31% helix, 33% strand	Q6V2E7
G	Fusion glycoprotein F0	protein	453	30% helix, 33% strand	Q6V2E7
H	Fusion glycoprotein F0	protein	451	31% helix, 33% strand	Q6V2E7
I	Fusion glycoprotein F0	protein	448	30% helix, 33% strand	Q6V2E7
J	MEDI8897 Fab heavy chain	protein	224	7% helix, 52% strand	—
K	MEDI8897 Fab heavy chain	protein	220	7% helix, 52% strand	—
L, M, N	MEDI8897 Fab heavy chain	protein	221	5% helix, 53% strand	—
O	MEDI8897 Fab heavy chain	protein	216	7% helix, 52% strand	—
P	MEDI8897 Fab light chain	protein	212	6% helix, 51% strand	—
Q, R, S, T	MEDI8897 Fab light chain	protein	211	6% helix, 52% strand	—
U	MEDI8897 Fab light chain	protein	208	6% helix, 51% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 15 copies · chains A, B, C, H, D, E, G, I, J, L

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	891	0.83	0.85	67	empty
2	1077	0.83	0.84	73	empty
3	756	0.83	0.86	61	empty
4	754	0.82	0.86	70	SO4
5	916	0.82	0.84	65	empty

Interfaces

53 interfaces between chains.

D–E · 2881 Å² buried · 27 hydrogen bonds · protein-protein
G–H · 2804 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 2631 Å² buried · 26 hydrogen bonds · protein-protein
A–C · 2412 Å² buried · 24 hydrogen bonds · protein-protein
H–I · 2402 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 96 disulfide (disulfide).

Compared structures

5UDD · Crystal Structure of RSV F B9320 Bound to MEDI8897 · 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 Q6V2E7
Elsewhere: RCSB PDB 5UDD · PDBe 5UDD · UniProt Q6V2E7

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