MolNFT v1 · #70991 · protein

Structure of S100A4 with pcp

3M0W · Protein S100-A4: “Structure of S100A4 with pcp”. X-ray diffraction, 2 ligands (P77, CA), 5 pockets (best druggability 0.73). MolNFT v1 #70991 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3M0W
Type: protein
Length: 891 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein S100-A4
UniProt: P26447
Ligands: P77, CA
Pockets: 5 · best druggability 0.73

Structure

x-ray diffraction · 8 distinct chains · 67% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Protein S100-A4	protein	90	69% helix, 4% strand	P26447
B	Protein S100-A4	protein	90	64% helix, 4% strand	P26447
C	Protein S100-A4	protein	88	67% helix, 5% strand	P26447
D	Protein S100-A4	protein	86	66% helix, 5% strand	P26447
F	Protein S100-A4	protein	86	67% helix, 5% strand	P26447
G	Protein S100-A4	protein	86	66% helix, 5% strand	P26447
H, I	Protein S100-A4	protein	93	67% helix, 4% strand	P26447
J	Protein S100-A4	protein	89	65% helix, 2% strand	P26447

Ligands and binding sites

P77 · 2-chloro-10-[3-(4-methylpiperazin-1-yl)propyl]-10H-phenothiazine · ligand · 12 copies · chains A, B, I, J, C, D, E, F, G, H
CA · Calcium ion · metal · 20 copies · chains A, B, C, D, E, F, G, H, I, J
DIO · 1,4-diethylene dioxide · additive · 2 copies · chains A, C, B, J

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

Pockets

5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1107	0.73	0.76	74	P77
2	857	0.73	0.77	60	P77, DIO
3	891	0.72	0.76	57	DIO, P77
4	752	0.71	0.77	39	P77
5	752	0.69	0.75	49	P77

Interfaces

15 interfaces between chains.

I–J · 1498 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1486 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 1486 Å² buried · 10 hydrogen bonds · protein-protein
G–H · 1484 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 1474 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

3M0W · Structure of S100A4 with PCP · the same entry in another collection · chain J against J, TM-score 1.00
P26447 · AlphaFold monomer V2.0 prediction for protein S100-A4 (P26447) · a predicted model of the same protein · chain F against A, TM-score 0.93

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 P26447
Elsewhere: RCSB PDB 3M0W · PDBe 3M0W · UniProt P26447

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