MolNFT v1 · #156273 · protein

CD146 D4-D5/AA98 Fab

6LYN · AA98 Fab heavy chain: “CD146 D4-D5/AA98 Fab”. X-ray diffraction, 3 ligands (NAG, CL, PO4), 11 pockets (best druggability 0.64). MolNFT v1 #156273 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6LYN
Type: protein
Length: 1,224 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: AA98 Fab heavy chain; AA98 Fab light chain; Cell surface glycoprotein MUC18
UniProt: P43121
Ligands: NAG, CL, PO4
Pockets: 11 · best druggability 0.64

Structure

x-ray diffraction · 5 distinct chains · 5% helix, 56% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, H	AA98 Fab heavy chain	protein	212	7% helix, 54% strand	—
B	AA98 Fab light chain	protein	218	5% helix, 52% strand	—
C	Cell surface glycoprotein MUC18	protein	183	5% helix, 60% strand	P43121
L	AA98 Fab light chain	protein	217	3% helix, 53% strand	—
D	Cell surface glycoprotein MUC18	protein	182	5% helix, 62% strand	P43121

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains C, D
CL · Chloride ion · ion · 4 copies · chains A, D
PO4 · Phosphate ion · ion · 2 copies · chains A, B, C, H
GOL · Glycerol · additive · 3 copies · chains A, B, C
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains B, C, L, D

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

Pockets

11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	474	0.64	0.77	64	EPE, CL, PO4
2	588	0.63	0.75	56	empty
3	567	0.61	0.74	73	empty
4	170	0.59	0.82	24	PO4
5	189	0.55	0.80	25	empty

Interfaces

9 interfaces between chains.

L–H · 1916 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1864 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 494 Å² buried · 6 hydrogen bonds · protein-protein
D–H · 491 Å² buried · 5 hydrogen bonds · protein-protein
L–D · 352 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

6LYN · CD146 D4-D5/AA98 Fab · the same entry in another collection · chain H against H, TM-score 1.00
P43121 · AlphaFold monomer V2.0 prediction for cell surface glycoprotein MUC18 (P43121) · a predicted model of the same protein · chain C against A, TM-score 0.69

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 P43121
Elsewhere: RCSB PDB 6LYN · PDBe 6LYN · UniProt P43121

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