MolNFT v1 · #15625 · protein

IGG1 Fab fragment (83.1) complex with 16-residue peptide (residues 304-321 of HIV-1 GP120 (mn isolate))

1NAK · Fab 83.1 - light chain: “IGG1 Fab fragment (83.1) complex with 16-residue peptide (residues 304-321 of HIV-1 GP120 (mn isolate))”. X-ray diffraction, 13 pockets (best druggability 0.73). MolNFT v1 #15625 on GenesisL1: 3D structure…

PDB: 1NAK
Type: protein
Length: 882 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab 83.1 - light chain; Fab 83.1 - heavy chain; Peptide MP1
Pockets: 13 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, M	Fab 83.1 - light chain	protein	217	6% helix, 51% strand	—
H, I	Fab 83.1 - heavy chain	protein	214	6% helix, 53% strand	—
P, Q	Peptide MP1	protein	10	0% helix, 0% strand	—

Pockets

13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	697	0.73	0.79	54	empty
2	720	0.73	0.79	94	empty
3	192	0.59	0.82	38	empty
4	324	0.58	0.77	47	empty
5	174	0.53	0.79	31	empty

Interfaces

9 interfaces between chains.

M–I · 1715 Å² buried · 15 hydrogen bonds · protein-protein
L–H · 1680 Å² buried · 14 hydrogen bonds · protein-protein
H–I · 821 Å² buried · 2 hydrogen bonds · protein-protein
I–Q · 360 Å² buried · 7 hydrogen bonds · protein-protein
H–P · 327 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

1NAK · IGG1 Fab fragment (83.1) complex with 16-residue peptide (residues 304-321 of HIV-1 GP120… · the same entry in another collection · chain L against L, 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 1NAK · PDBe 1NAK

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