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X-ray structure of macrophage inflammatory protein-1 alpha polymer

Analyse X-ray structure of macrophage inflammatory protein-1 alpha polymer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2X69
Type: protein
Length: 330 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 0.69

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	C-C motif chemokine 3	protein	66	21% helix, 23% 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	83	0.69	0.94	20	empty
2	418	0.68	0.80	61	empty
3	110	0.67	0.90	28	empty
4	109	0.54	0.83	29	empty

Interfaces

7 interfaces between chains.

B–C · 717 Å² buried · 9 hydrogen bonds · protein-protein
D–E · 693 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 621 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 591 Å² buried · 8 hydrogen bonds · protein-protein
C–E · 548 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

2X69 · X-ray Structure of Macrophage Inflammatory Protein-1 alpha polymer · 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 2X69 · PDBe 2X69 · UniProt P10147

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