MolNFT v1 · #121126 · protein

Llama vhh 2E7 in complex with GP41

5HM1 · Lama vhh antibody 2E7: “Llama vhh 2E7 in complex with GP41”. X-ray diffraction, 2 pockets (best druggability 0.62). MolNFT v1 #121126 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5HM1
Type: protein
Length: 402 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lama vhh antibody 2E7; GP41
UniProt: P04578
Pockets: 2 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 13% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Lama vhh antibody 2E7	protein	119	5% helix, 55% strand	—
D, E, F	GP41	protein	15	80% helix, 0% strand	P04578

Pockets

2 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	158	0.62	0.85	31	empty
2	308	0.58	0.77	35	empty

Interfaces

6 interfaces between chains.

A–D · 655 Å² buried · 5 hydrogen bonds · protein-protein
B–E · 655 Å² buried · 5 hydrogen bonds · protein-protein
C–F · 645 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 546 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 346 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5HM1 · Llama VHH 2E7 in complex with gp41 · 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 P04578
Elsewhere: RCSB PDB 5HM1 · PDBe 5HM1 · UniProt P04578

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