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Crystal structure of DH511.2_K3 Fab in complex with HIV-1 GP41 mper peptide

Analyse Crystal structure of DH511.2_K3 Fab in complex with HIV-1 GP41 mper peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5U3O
Type: protein
Length: 468 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DH511.2_K3 Fab heavy chain; DH511.2_K3 Fab light chain; GP41 mper peptide
Pockets: 5 · best druggability 0.54

Structure

x-ray diffraction · 3 distinct chains · 11% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	DH511.2_K3 Fab heavy chain	protein	235	10% helix, 52% strand	—
L	DH511.2_K3 Fab light chain	protein	216	7% helix, 49% strand	—
A	GP41 mper peptide	protein	17	71% helix, 0% strand	—

Pockets

5 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	53	0.54	0.89	20	empty
2	109	0.51	0.81	21	empty
3	278	0.49	0.73	44	empty
4	94	0.33	0.73	17	empty
5	69	0.30	0.74	18	empty

Interfaces

2 interfaces between chains.

H–L · 2226 Å² buried · 25 hydrogen bonds · protein-protein
H–A · 705 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5U3O · Crystal Structure of DH511.2_K3 Fab in Complex with HIV-1 gp41 MPER Peptide · the same entry in another collection · chain H against H, 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 5U3O · PDBe 5U3O

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