MolNFT v1 · #135591 · protein

Crystal structure of DH511.11P Fab in complex with HIV-1 GP41 mper peptide

5U3M · DH511.11P Fab heavy chain: “Crystal structure of DH511.11P Fab in complex with HIV-1 GP41 mper peptide”. X-ray diffraction, 6 pockets (best druggability 0.58). MolNFT v1 #135591 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5U3M
Type: protein
Length: 476 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DH511.11P Fab heavy chain; DH511.11P Fab light chain; GP41 mper peptide
Pockets: 6 · best druggability 0.58

Structure

x-ray diffraction · 3 distinct chains · 12% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	DH511.11P Fab heavy chain	protein	235	13% helix, 51% strand	—
L	DH511.11P Fab light chain	protein	216	8% helix, 49% strand	—
A	GP41 mper peptide	protein	25	48% helix, 0% strand	—

Pockets

6 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	405	0.58	0.75	35	empty
2	50	0.54	0.90	17	empty
3	142	0.41	0.74	29	empty
4	103	0.38	0.75	24	empty
5	77	0.36	0.76	15	empty

Interfaces

2 interfaces between chains.

H–L · 2190 Å² buried · 25 hydrogen bonds · protein-protein
H–A · 713 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

5U3M · Crystal Structure of DH511.11P 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 5U3M · PDBe 5U3M

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