MolNFT v1 · #191058 · protein

PTX3 pentraxin domain

7ZL1 · Pentraxin-related protein PTX3: “PTX3 pentraxin domain”. Electron microscopy, 1 ligand (NAG), 19 pockets (best druggability 0.79). MolNFT v1 #191058 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7ZL1
Type: protein
Length: 1,720 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pentraxin-related protein PTX3
UniProt: P26022
Ligands: NAG
Pockets: 19 · best druggability 0.79

Structure

electron microscopy · 1 distinct chain · 10% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A, D, C, E, H, G, F	Pentraxin-related protein PTX3	protein	215	10% helix, 40% strand	P26022

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains B, A, D, C, E, H, G, F

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

Pockets

19 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	764	0.79	0.83	59	empty
2	784	0.77	0.81	61	empty
3	942	0.77	0.79	135	empty
4	223	0.66	0.84	32	empty
5	244	0.65	0.83	37	empty

Interfaces

17 interfaces between chains.

E–F · 824 Å² buried · 11 hydrogen bonds · protein-protein
D–C · 823 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 822 Å² buried · 9 hydrogen bonds · protein-protein
E–H · 821 Å² buried · 12 hydrogen bonds · protein-protein
B–A · 819 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 disulfide, 8 glycan (disulfide, N-glycosylation).

Compared structures

7ZL1 · PTX3 Pentraxin Domain · the same entry in another collection · chain F against F, TM-score 1.00
P26022 · AlphaFold monomer V2.0 prediction for pentraxin-related protein PTX3 (P26022) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 P26022
Elsewhere: RCSB PDB 7ZL1 · PDBe 7ZL1 · UniProt P26022

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