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Crystal structure of the MRP14 complexed with chaps

Analyse Crystal structure of the MRP14 complexed with chaps in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1IRJ
Type: protein
Length: 670 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Migration inhibitory factor-related protein 14
UniProt: P06702
Ligands: CPS, CA
Pockets: 4 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 62% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, H	Migration inhibitory factor-related protein 14	protein	85	60% helix, 2% strand	P06702
B, F, G	Migration inhibitory factor-related protein 14	protein	84	62% helix, 2% strand	P06702
C, E	Migration inhibitory factor-related protein 14	protein	83	63% helix, 2% strand	P06702
D	Migration inhibitory factor-related protein 14	protein	82	63% helix, 2% strand	P06702

Ligands and binding sites

CPS · 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate · ligand · 4 copies · chains B, G, D, E
CA · Calcium ion · metal · 16 copies · chains A, B, C, D, E, F, G, H

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

Pockets

4 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	1024	0.76	0.78	79	empty
2	264	0.58	0.79	37	empty
3	161	0.43	0.74	23	CPS
4	158	0.43	0.74	24	CPS

Interfaces

9 interfaces between chains.

G–H · 1337 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1291 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 1281 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 1258 Å² buried · 7 hydrogen bonds · protein-protein
B–E · 469 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

1IRJ · Crystal Structure of the MRP14 complexed with CHAPS · the same entry in another collection · chain H against H, TM-score 1.00
P06702 · AlphaFold monomer V2.0 prediction for protein S100-A9 (P06702) · a predicted model of the same protein · chain D against A, TM-score 0.97

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 P06702
Elsewhere: RCSB PDB 1IRJ · PDBe 1IRJ · UniProt P06702

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