MolNFT v1 · #181678 · protein

Cryo-EM structure of the hcmv pentamer bound by human neuropilin 2

7M22 · Envelope protein UL128: “Cryo-EM structure of the hcmv pentamer bound by human neuropilin 2”. Electron microscopy, 2 ligands (NAG, CA), 7 pockets (best druggability 0.75). MolNFT v1 #181678 on GenesisL1: 3D structure, binding sites…

PDB: 7M22
Type: protein
Length: 748 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Envelope protein UL128; Envelope glycoprotein UL130; UL131A; Neuropilin-2
UniProt: C8BLJ3, A0A0G2TB82, Q38M21, O60462
Ligands: NAG, CA
Pockets: 7 · best druggability 0.75

Structure

electron microscopy · 4 distinct chains · 16% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Envelope protein UL128	protein	107	22% helix, 22% strand	C8BLJ3
D	Envelope glycoprotein UL130	protein	111	27% helix, 35% strand	A0A0G2TB82
E	UL131A	protein	108	45% helix, 19% strand	Q38M21
N	Neuropilin-2	protein	422	4% helix, 45% strand	O60462

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains C, E, N
CA · Calcium ion · metal · chains C, N

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

Pockets

7 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	472	0.75	0.84	60	empty
2	601	0.68	0.77	65	empty
3	201	0.64	0.84	37	empty
4	51	0.54	0.89	16	empty
5	98	0.53	0.83	21	empty

Interfaces

6 interfaces between chains.

D–E · 2584 Å² buried · 35 hydrogen bonds · protein-protein
C–D · 1002 Å² buried · 9 hydrogen bonds · protein-protein
C–E · 925 Å² buried · 7 hydrogen bonds · protein-protein
C–N · 472 Å² buried · 3 hydrogen bonds · protein-protein
E–N · 234 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

7M22 · Cryo-EM structure of the HCMV pentamer bound by human neuropilin 2 · the same entry in another collection · chain C against C, TM-score 1.00
O60462 · AlphaFold monomer V2.0 prediction for neuropilin-2 (O60462) · a predicted model of the same protein · chain N against A, TM-score 0.98

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 C8BLJ3
Every structure of UniProt A0A0G2TB82
Every structure of UniProt Q38M21
Every structure of UniProt O60462
Elsewhere: RCSB PDB 7M22 · PDBe 7M22 · UniProt C8BLJ3 · UniProt A0A0G2TB82 · UniProt Q38M21 · UniProt O60462

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