MolNFT v1 · #137811 · protein

Anti-tissue factor antibody M59, a humanized version of 10H10

5W05 · M59 Fab light chain: “Anti-tissue factor antibody M59, a humanized version of 10H10”. X-ray diffraction, 5 pockets (best druggability 0.58). MolNFT v1 #137811 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5W05
Type: protein
Length: 439 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: M59 Fab light chain; M59 Fab heavy chain
Pockets: 5 · best druggability 0.58

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	M59 Fab light chain	protein	219	6% helix, 50% strand	—
H	M59 Fab heavy chain	protein	220	11% helix, 52% strand	—

Ligands and binding sites

PEG · Di(hydroxyethyl)ether · additive · chains L, H

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

Pockets

5 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	436	0.58	0.74	50	PEG
2	57	0.52	0.88	22	empty
3	106	0.37	0.74	24	empty
4	94	0.33	0.73	21	empty
5	61	0.31	0.75	18	empty

Interfaces

1 interface between chains.

L–H · 1994 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5W05 · Anti-tissue factor antibody M59, a humanized version of 10H10 · 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 5W05 · PDBe 5W05

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