MolNFT v1 · #153938 · protein

Crystal structure of human CRMP2 1-532, unmodified

6JV9 · Dihydropyrimidinase-related protein 2: “Crystal structure of human CRMP2 1-532, unmodified”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.86). MolNFT v1 #153938 on GenesisL1: 3D structure, binding sites and…

PDB: 6JV9
Type: protein
Length: 1,947 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dihydropyrimidinase-related protein 2
UniProt: Q16555
Ligands: SO4
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 4 distinct chains · 35% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dihydropyrimidinase-related protein 2	protein	486	35% helix, 23% strand	Q16555
B	Dihydropyrimidinase-related protein 2	protein	495	35% helix, 23% strand	Q16555
C	Dihydropyrimidinase-related protein 2	protein	483	36% helix, 23% strand	Q16555
D	Dihydropyrimidinase-related protein 2	protein	483	36% helix, 23% strand	Q16555

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A, D, B
DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains B
EDO · 1,2-ethanediol · additive · chains B, C
PGE · Triethylene glycol · additive · chains D

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	800	0.86	0.89	82	empty
2	765	0.85	0.89	81	empty
3	366	0.72	0.84	33	empty
4	343	0.72	0.84	34	empty
5	258	0.66	0.82	34	empty

Interfaces

5 interfaces between chains.

A–B · 2156 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 1647 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 1256 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 1236 Å² buried · 19 hydrogen bonds · protein-protein
B–D · 17 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6JV9 · Crystal Structure of Human CRMP2 1-532, unmodified · the same entry in another collection · chain D against D, TM-score 1.00
Q16555 · AlphaFold monomer V2.0 prediction for dihydropyrimidinase-related protein 2 (Q16555) · a predicted model of the same protein · chain C against A, TM-score 1.00

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 Q16555
Elsewhere: RCSB PDB 6JV9 · PDBe 6JV9 · UniProt Q16555

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