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Crystal structure of S25-39 Fab in complex with 4-meo-kdooall

Analyse Crystal structure of S25-39 Fab in complex with 4-meo-kdooall in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7T0F
Type: protein
Length: 432 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: S25-39 Fab heavy chain; S25-39 Fab light chain
Ligands: K71
Pockets: 4 · best druggability 0.58

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	S25-39 Fab heavy chain	protein	214	10% helix, 50% strand	—
L	S25-39 Fab light chain	protein	218	6% helix, 53% strand	—

Ligands and binding sites

K71 · 3-deoxy-4-O-methyl-alpha-D-manno-oct-2-ulopyranosonic acid · ligand · chains H, L

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	408	0.58	0.75	57	empty
2	69	0.47	0.84	21	empty
3	106	0.34	0.73	20	empty
4	59	0.29	0.74	14	empty

Interfaces

1 interface between chains.

H–L · 1816 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7T0F · Crystal structure of S25-39 Fab in complex with 4-MeO-KdoOAll · 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 7T0F · PDBe 7T0F

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