MolNFT v1 · #105622 · protein

Structure analysis of the MIP1A P8A mutant

4RA8 · C-C motif chemokine 3: “Structure analysis of the MIP1A P8A mutant”. X-ray diffraction, 4 pockets (best druggability 0.76). MolNFT v1 #105622 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4RA8
Type: protein
Length: 336 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: C-C motif chemokine 3
UniProt: P10147
Pockets: 4 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 21% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	C-C motif chemokine 3	protein	68	21% helix, 22% strand	P10147
B	C-C motif chemokine 3	protein	69	20% helix, 26% strand	P10147
C	C-C motif chemokine 3	protein	66	23% helix, 27% strand	P10147
D	C-C motif chemokine 3	protein	65	22% helix, 28% strand	P10147

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	342	0.76	0.87	48	empty
2	347	0.73	0.85	44	empty
3	177	0.63	0.84	32	empty
4	127	0.61	0.86	28	empty

Interfaces

8 interfaces between chains.

A–B · 731 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 653 Å² buried · 7 hydrogen bonds · protein-protein
D–E · 636 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 594 Å² buried · 9 hydrogen bonds · protein-protein
B–E · 563 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

4RA8 · Structure analysis of the Mip1a P8A mutant · 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 D 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 4RA8 · PDBe 4RA8 · UniProt P10147

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