MolNFT v1 · #135592 · protein

Crystal structure of DH511.12P Fab in complex with HIV-1 GP41 mper peptide

5U3N · DH511.12P Fab heavy chain: “Crystal structure of DH511.12P Fab in complex with HIV-1 GP41 mper peptide”. X-ray diffraction, 4 pockets (best druggability 0.62). MolNFT v1 #135592 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5U3N
Type: protein
Length: 472 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DH511.12P Fab heavy chain; DH511.12P Fab light chain; GP41 mper peptide
Pockets: 4 · best druggability 0.62

Structure

x-ray diffraction · 3 distinct chains · 11% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	DH511.12P Fab heavy chain	protein	234	12% helix, 51% strand	—
L	DH511.12P Fab light chain	protein	215	6% helix, 50% strand	—
A	GP41 mper peptide	protein	23	52% helix, 0% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	624	0.62	0.74	62	empty
2	89	0.38	0.76	19	empty
3	97	0.37	0.75	19	empty
4	63	0.33	0.76	14	empty

Interfaces

2 interfaces between chains.

H–L · 2094 Å² buried · 22 hydrogen bonds · protein-protein
H–A · 705 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5U3N · Crystal Structure of DH511.12P 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 5U3N · PDBe 5U3N

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