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X-ray structure of macrophage inflammatory protein-1 beta

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

PDB: 2X6L
Type: protein
Length: 328 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: C-C motif chemokine 4
UniProt: P13236
Pockets: 5 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 23% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E	C-C motif chemokine 4	protein	66	23% helix, 23% strand	P13236
B, D	C-C motif chemokine 4	protein	65	23% helix, 28% strand	P13236

Ligands and binding sites

GOL · Glycerol · additive · 3 copies · chains B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	135	0.62	0.86	23	empty
2	252	0.57	0.78	26	empty
3	157	0.57	0.82	25	empty
4	71	0.43	0.81	17	empty
5	139	0.40	0.74	24	empty

Interfaces

7 interfaces between chains.

C–E · 710 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 703 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 573 Å² buried · 14 hydrogen bonds · protein-protein
B–E · 566 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 491 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

2X6L · X-ray Structure of Macrophage Inflammatory Protein-1 beta · the same entry in another collection · chain E against E, TM-score 1.00
P13236 · AlphaFold monomer V2.0 prediction for C-C motif chemokine 4 (P13236) · a predicted model of the same protein · chain B 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 P13236
Elsewhere: RCSB PDB 2X6L · PDBe 2X6L · UniProt P13236

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