MolNFT v1 · #142605 · protein

Crystal structure of the complex of the hydrolytic antibody Fab 9C10 with a transition-state analog

6A9K · Immunoglobulin 9C10 L chain: “Crystal structure of the complex of the hydrolytic antibody Fab 9C10 with a transition-state analog”. X-ray diffraction, 1 ligand (9T0), 10 pockets (best druggability 0.81). MolNFT v1 #142605 on…

PDB: 6A9K
Type: protein
Length: 878 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Immunoglobulin 9C10 L chain; Immunoglobulin 9C10 H chain
Ligands: 9T0
Pockets: 10 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, A	Immunoglobulin 9C10 L chain	protein	219	6% helix, 51% strand	—
H, B	Immunoglobulin 9C10 H chain	protein	220	8% helix, 51% strand	—

Ligands and binding sites

9T0 · 5-[(2R,3R)-2-[2,2-bis(chloranyl)ethanoylamino]-3-(4-nitrophenyl)-3-[oxidanyl-[[4-[2,2,2-tris(fluoranyl) ethanoylamino]phenyl]methyl]phosphoryl]oxy-propoxy]-5-oxidanylidene-pentanoic acid · ligand · 2 copies · chains L, H, A, B

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

Pockets

10 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	1047	0.81	0.82	112	empty
2	584	0.65	0.76	55	empty
3	664	0.64	0.74	69	empty
4	144	0.52	0.79	18	9T0
5	149	0.52	0.79	22	9T0

Interfaces

6 interfaces between chains.

L–H · 1938 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1935 Å² buried · 19 hydrogen bonds · protein-protein
L–B · 271 Å² buried · 3 hydrogen bonds · protein-protein
H–A · 196 Å² buried · 2 hydrogen bonds · protein-protein
L–A · 159 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

6A9K · Crystal structure of the complex of the hydrolytic antibody Fab 9C10 with a… · 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 6A9K · PDBe 6A9K

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