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Structure of the tfp-CA2+-bound activated form of the S100A4 metastasis factor

Analyse Structure of the tfp-CA2+-bound activated form of the S100A4 metastasis factor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3KO0
Type: protein
Length: 1,846 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein S100-A4
UniProt: P26447
Ligands: TFP, CA
Pockets: 12 · best druggability 0.77

Structure

x-ray diffraction · 6 distinct chains · 67% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, I, J, K, L, O, R, S, T	Protein S100-A4	protein	93	67% helix, 2% strand	P26447
E, M, N, P	Protein S100-A4	protein	92	68% helix, 2% strand	P26447
F	Protein S100-A4	protein	90	69% helix, 4% strand	P26447
G	Protein S100-A4	protein	90	69% helix, 2% strand	P26447
H	Protein S100-A4	protein	94	66% helix, 4% strand	P26447
Q	Protein S100-A4	protein	88	66% helix, 5% strand	P26447

Ligands and binding sites

TFP · 10-[3-(4-methyl-piperazin-1-yl)-propyl]-2-trifluoromethyl-10H-phenothiazine · ligand · 40 copies · chains A, C, B, D, J, I, E, F, G, H, K, S, L, T, N, M, P, O, Q, R
CA · Calcium ion · metal · 40 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T

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

Pockets

12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	904	0.77	0.79	61	TFP
2	1091	0.76	0.78	74	TFP
3	1141	0.75	0.78	84	TFP
4	811	0.75	0.79	55	TFP
5	1043	0.75	0.77	67	TFP

Interfaces

43 interfaces between chains.

I–J · 1475 Å² buried · 10 hydrogen bonds · protein-protein
M–N · 1471 Å² buried · 9 hydrogen bonds · protein-protein
K–L · 1468 Å² buried · 10 hydrogen bonds · protein-protein
Q–R · 1467 Å² buried · 10 hydrogen bonds · protein-protein
O–P · 1460 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

3KO0 · Structure of the tfp-ca2+-bound activated form of the s100a4 Metastasis factor · the same entry in another collection · chain J against J, 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 P26447
Elsewhere: RCSB PDB 3KO0 · PDBe 3KO0 · UniProt P26447

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