MolNFT v1 · #123578 · protein

Crystal structure of unbound anti-glycan antibody FAB14.22 at 2.2 a

5JOR · FAB14.22 heavy chain: “Crystal structure of unbound anti-glycan antibody FAB14.22 at 2.2 a”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.82). MolNFT v1 #123578 on GenesisL1: 3D structure, binding sites and…

PDB: 5JOR
Type: protein
Length: 1,708 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: FAB14.22 heavy chain; Fab 14.22 light chain
Ligands: SO4
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 5 distinct chains · 5% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	FAB14.22 heavy chain	protein	207	9% helix, 54% strand	—
A, L, C	Fab 14.22 light chain	protein	218	5% helix, 52% strand	—
F, H	FAB14.22 heavy chain	protein	211	3% helix, 56% strand	—
D	FAB14.22 heavy chain	protein	208	3% helix, 54% strand	—
E	Fab 14.22 light chain	protein	217	6% helix, 52% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 19 copies · chains B, C, A, D, F, L, H, E
GOL · Glycerol · additive · 33 copies · chains B, C, A, L, D, F, E, H
1PE · Pentaethylene glycol · additive · 15 copies · chains B, C, A, F, H, D, L, E

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

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	812	0.82	0.85	81	1PE, GOL
2	349	0.71	0.83	46	GOL
3	641	0.67	0.77	56	empty
4	590	0.67	0.77	54	SO4, GOL, 1PE
5	148	0.67	0.88	29	GOL

Interfaces

13 interfaces between chains.

H–L · 1887 Å² buried · 20 hydrogen bonds · protein-protein
F–E · 1870 Å² buried · 21 hydrogen bonds · protein-protein
A–D · 1815 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 1812 Å² buried · 17 hydrogen bonds · protein-protein
L–D · 563 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 2 covalent (disulfide, additive adduct).

Compared structures

5JOR · Crystal structure of unbound anti-glycan antibody Fab14.22 at 2.2 A · the same entry in another collection · chain E against E, 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 5JOR · PDBe 5JOR

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