MolNFT v1 · #63080 · protein

Crystal structure of anti-human cytomegalovirus antibody 8F9

3EYO · 8F9 Fab: “Crystal structure of anti-human cytomegalovirus antibody 8F9”. X-ray diffraction, 7 pockets (best druggability 0.55). MolNFT v1 #63080 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3EYO
Type: protein
Length: 857 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 8F9 Fab; Ad-2
Pockets: 7 · best druggability 0.55

Structure

x-ray diffraction · 4 distinct chains · 6% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	8F9 Fab	protein	213	7% helix, 50% strand	—
B	Ad-2	protein	212	4% helix, 51% strand	—
C	8F9 Fab	protein	214	5% helix, 49% strand	—
D	Ad-2	protein	218	7% helix, 50% strand	—

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	333	0.55	0.75	38	empty
2	299	0.52	0.74	42	empty
3	85	0.34	0.74	22	empty
4	93	0.33	0.73	20	empty
5	73	0.32	0.75	20	empty

Interfaces

3 interfaces between chains.

C–D · 1712 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1623 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 584 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

3EYO · Crystal structure of anti-human cytomegalovirus antibody 8F9 · the same entry in another collection · chain D against D, 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
Elsewhere: RCSB PDB 3EYO · PDBe 3EYO

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