MolNFT v1 · #75150 · protein

Crystal structure of S64-4 in complex with kdo

3PHQ · S64-4 Fab (IGG1) light chain: “Crystal structure of S64-4 in complex with kdo”. X-ray diffraction, 1 ligand (KDO), 3 pockets (best druggability 0.63). MolNFT v1 #75150 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3PHQ
Type: protein
Length: 429 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: S64-4 Fab (IGG1) light chain; S64-4 Fab (IGG1) heavy chain
Ligands: KDO
Pockets: 3 · best druggability 0.63

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	S64-4 Fab (IGG1) light chain	protein	216	7% helix, 52% strand	—
B	S64-4 Fab (IGG1) heavy chain	protein	213	7% helix, 50% strand	—

Ligands and binding sites

KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid · sugar · chains A, B

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

Pockets

3 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	558	0.63	0.75	60	empty
2	59	0.31	0.75	14	empty
3	53	0.27	0.74	12	empty

Interfaces

1 interface between chains.

A–B · 1702 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

3PHQ · Crystal structure of S64-4 in complex with KDO · the same entry in another collection · chain B against B, 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 3PHQ · PDBe 3PHQ

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