MolNFT v1 · #96636 · protein

Crystal structure of a putative VRC01 germline precursor Fab

4JPI · Putative VRC01 germline Fab heavy chain: “Crystal structure of a putative VRC01 germline precursor Fab”. X-ray diffraction, 6 pockets (best druggability 0.81). MolNFT v1 #96636 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4JPI
Type: protein
Length: 849 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative VRC01 germline Fab heavy chain; Putative VRC01 germline Fab light chain
Pockets: 6 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 9% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Putative VRC01 germline Fab heavy chain	protein	221	12% helix, 50% strand	—
L	Putative VRC01 germline Fab light chain	protein	206	6% helix, 51% strand	—
A	Putative VRC01 germline Fab heavy chain	protein	215	11% helix, 53% strand	—
B	Putative VRC01 germline Fab light chain	protein	207	6% helix, 51% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 5 copies · chains H, B, L, A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1140	0.81	0.82	124	GOL
2	344	0.57	0.76	43	empty
3	59	0.55	0.89	21	empty
4	137	0.45	0.77	20	empty
5	74	0.30	0.73	22	empty

Interfaces

4 interfaces between chains.

H–L · 1891 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1628 Å² buried · 16 hydrogen bonds · protein-protein
L–B · 777 Å² buried · 11 hydrogen bonds · protein-protein
H–B · 145 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

4JPI · Crystal structure of a putative VRC01 germline precursor Fab · the same entry in another collection · chain A against A, 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 4JPI · PDBe 4JPI

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