MolNFT v1 · #68973 · protein

Human macrophage inflammatory protein-1 alpha L3M_V63M

3KBX · CCL3: “Human macrophage inflammatory protein-1 alpha L3M_V63M”. X-ray diffraction, 1 ligand (K), 3 pockets (best druggability 0.63). MolNFT v1 #68973 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3KBX
Type: protein
Length: 330 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CCL3
UniProt: P10147
Ligands: K
Pockets: 3 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 21% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	CCL3	protein	66	21% helix, 23% strand	P10147

Ligands and binding sites

K · Potassium ion · metal · chains A
ACT · Acetate ion · additive · chains A

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	52	0.63	0.94	16	empty
2	219	0.60	0.81	34	empty
3	88	0.42	0.79	18	empty

Interfaces

7 interfaces between chains.

D–E · 729 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 712 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 640 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 630 Å² buried · 8 hydrogen bonds · protein-protein
C–E · 626 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 5 modified (disulfide, engineered).

Compared structures

3KBX · Human macrophage inflammatory protein-1 alpha L3M_V63M · the same entry in another collection · chain E against E, TM-score 1.00
P10147 · AlphaFold monomer V2.0 prediction for C-C motif chemokine 3 (P10147) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P10147
Elsewhere: RCSB PDB 3KBX · PDBe 3KBX · UniProt P10147

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