MolNFT v1 · #135588 · protein

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

5U3J · DH511.1 heavy chain: “Crystal structure of DH511.1 Fab in complex with HIV-1 GP41 mper peptide”. X-ray diffraction, 6 pockets (best druggability 0.57). MolNFT v1 #135588 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5U3J
Type: protein
Length: 479 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DH511.1 heavy chain; DH511.1 light chain; GP41 mper peptide
Pockets: 6 · best druggability 0.57

Structure

x-ray diffraction · 3 distinct chains · 11% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	DH511.1 heavy chain	protein	235	10% helix, 50% strand	—
L	DH511.1 light chain	protein	215	7% helix, 48% strand	—
A	GP41 mper peptide	protein	29	55% helix, 0% strand	—

Pockets

6 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	426	0.57	0.74	56	empty
2	100	0.45	0.79	26	empty
3	77	0.42	0.80	16	empty
4	84	0.35	0.75	19	empty
5	79	0.31	0.73	25	empty

Interfaces

2 interfaces between chains.

H–L · 2118 Å² buried · 19 hydrogen bonds · protein-protein
H–A · 802 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5U3J · Crystal Structure of DH511.1 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 5U3J · PDBe 5U3J

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