MolNFT v1 · #175926 · protein

Crystal structure of EBV GH/GL bound with neutralizing antibody 1D8

7D5Z · Envelope glycoprotein H: “Crystal structure of EBV GH/GL bound with neutralizing antibody 1D8”. X-ray diffraction, 20 pockets (best druggability 0.83). MolNFT v1 #175926 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7D5Z
Type: protein
Length: 4,704 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Envelope glycoprotein H; Envelope glycoprotein L; Light chain of 1D8; Heavy chain of 1D8
UniProt: Q3KSQ3, Q3KSS3
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 26% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
M, A, E, I	Envelope glycoprotein H	protein	655	38% helix, 21% strand	Q3KSQ3
N, B, F, J	Envelope glycoprotein L	protein	94	30% helix, 15% strand	Q3KSS3
O, C, G, K	Light chain of 1D8	protein	213	6% helix, 52% strand	—
P, D, H, L	Heavy chain of 1D8	protein	214	6% helix, 50% strand	—

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	188	0.83	0.97	26	empty
2	191	0.82	0.97	26	empty
3	1144	0.74	0.77	105	empty
4	80	0.73	0.96	18	empty
5	78	0.73	0.96	20	empty

Interfaces

32 interfaces between chains.

I–J · 2245 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 2234 Å² buried · 24 hydrogen bonds · protein-protein
E–F · 2227 Å² buried · 24 hydrogen bonds · protein-protein
M–N · 2211 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 1788 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 44 disulfide (disulfide).

Compared structures

7D5Z · Crystal structure of EBV gH/gL bound with neutralizing antibody 1D8 · the same entry in another collection · chain M against M, 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 Q3KSQ3
Every structure of UniProt Q3KSS3
Elsewhere: RCSB PDB 7D5Z · PDBe 7D5Z · UniProt Q3KSQ3 · UniProt Q3KSS3

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