MolNFT v1 · #16738 · protein

Crystal structure of ip-10 M-form

1O7Y · Small inducible cytokine B10: “Crystal structure of ip-10 M-form”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.77). MolNFT v1 #16738 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1O7Y
Type: protein
Length: 254 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Small inducible cytokine B10
UniProt: P02778
Ligands: SO4
Pockets: 2 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 17% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Small inducible cytokine B10	protein	67	10% helix, 27% strand	P02778
B	Small inducible cytokine B10	protein	62	21% helix, 27% strand	P02778
C	Small inducible cytokine B10	protein	63	16% helix, 30% strand	P02778
D	Small inducible cytokine B10	protein	62	19% helix, 31% strand	P02778

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1150	0.77	0.79	94	empty
2	64	0.37	0.78	18	empty

Interfaces

6 interfaces between chains.

C–D · 689 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 640 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 488 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 272 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 155 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

1O7Y · Crystal structure of IP-10 M-form · the same entry in another collection · chain A against A, TM-score 1.00
P02778 · AlphaFold monomer V2.0 prediction for C-X-C motif chemokine 10 (P02778) · a predicted model of the same protein · chain D 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 P02778
Elsewhere: RCSB PDB 1O7Y · PDBe 1O7Y · UniProt P02778

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