MolNFT v1 · #60483 · protein

Crystal structure of the trimeric prefusion ebola virus glycoprotein in complex with a neutralizing antibody from a human survivor

3CSY · Fab KZ52 heavy chain: “Crystal structure of the trimeric prefusion ebola virus glycoprotein in complex with a neutralizing antibody…”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.87). MolNFT v1…

PDB: 3CSY
Type: protein
Length: 3,074 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab KZ52 heavy chain; Fab KZ52 light chain; Envelope glycoprotein GP1; Envelope…
UniProt: Q05320, P87666
Ligands: NAG, MAN, BMA
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 10 distinct chains · 15% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Fab KZ52 heavy chain	protein	226	4% helix, 46% strand	—
B, D, F, H	Fab KZ52 light chain	protein	217	5% helix, 49% strand	—
I	Envelope glycoprotein GP1	protein	236	11% helix, 39% strand	Q05320
J	Envelope glycoprotein GP2	protein	98	35% helix, 15% strand	P87666
K	Envelope glycoprotein GP1	protein	232	12% helix, 41% strand	Q05320
L	Envelope glycoprotein GP2	protein	93	37% helix, 11% strand	P87666
M	Envelope glycoprotein GP1	protein	230	10% helix, 39% strand	Q05320
N	Envelope glycoprotein GP2	protein	95	35% helix, 16% strand	P87666
O	Envelope glycoprotein GP1	protein	225	10% helix, 40% strand	Q05320
P	Envelope glycoprotein GP2	protein	93	37% helix, 13% strand	P87666

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains I, J, K, L, M, N, O, P
MAN · alpha-D-mannopyranose · sugar · 8 copies · chains L, N, J
BMA · beta-D-mannopyranose · sugar · 7 copies · chains K

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1025	0.87	0.88	109	empty
2	56	0.72	0.99	18	empty
3	64	0.72	0.98	19	empty
4	54	0.70	0.98	18	empty
5	778	0.67	0.75	85	empty

Interfaces

33 interfaces between chains.

K–L · 2424 Å² buried · 31 hydrogen bonds · protein-protein
I–J · 2419 Å² buried · 35 hydrogen bonds · protein-protein
M–N · 2411 Å² buried · 29 hydrogen bonds · protein-protein
O–P · 2408 Å² buried · 29 hydrogen bonds · protein-protein
G–H · 1966 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 28 disulfide, 20 modified, 7 glycan (disulfide, engineered, N-glycosylation).

Compared structures

3CSY · Crystal structure of the trimeric prefusion Ebola virus glycoprotein in complex with a… · 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 Q05320
Every structure of UniProt P87666
Elsewhere: RCSB PDB 3CSY · PDBe 3CSY · UniProt Q05320 · UniProt P87666

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