MolNFT v1 · #144818 · protein

S25-23 Fab in complex with chlamydiaceae lps (crystal form 1)

6C5J · IGG1 Fab heavy chain: “S25-23 Fab in complex with chlamydiaceae lps (crystal form 1)”. X-ray diffraction, 4 ligands (GP1, Z9M, KDO), 4 pockets (best druggability 0.67). MolNFT v1 #144818 on GenesisL1: 3D structure, binding sites and…

PDB: 6C5J
Type: protein
Length: 435 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: IGG1 Fab heavy chain; IGG1 Fab light chain (kappa)
UniProt: Q99LC4, A0A0F7R5U8
Ligands: GP1, Z9M, KDO, NAG
Pockets: 4 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	IGG1 Fab heavy chain	protein	218	10% helix, 53% strand	Q99LC4
L	IGG1 Fab light chain (kappa)	protein	217	6% helix, 51% strand	A0A0F7R5U8

Ligands and binding sites

GP1 · 2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose · ligand · chains L
Z9M · 2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose · ligand · chains H
KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid · sugar · 3 copies · chains H, L
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H

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	692	0.67	0.76	66	empty
2	100	0.36	0.74	22	empty
3	81	0.33	0.75	18	empty
4	51	0.25	0.74	14	empty

Interfaces

1 interface between chains.

H–L · 2076 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

6C5J · S25-23 Fab in complex with Chlamydiaceae LPS (Crystal form 1) · 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
Every structure of UniProt Q99LC4
Every structure of UniProt A0A0F7R5U8
Elsewhere: RCSB PDB 6C5J · PDBe 6C5J · UniProt Q99LC4 · UniProt A0A0F7R5U8

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.