MolNFT v1 · #51939 · protein

Human crmp-2 crystallised in the presence of mg

2VM8 · Dihydropyrimidinase-related protein 2: “Human crmp-2 crystallised in the presence of mg”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.85). MolNFT v1 #51939 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 2VM8
Type: protein
Length: 1,905 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dihydropyrimidinase-related protein 2
UniProt: Q16555
Ligands: MG
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dihydropyrimidinase-related protein 2	protein	477	37% helix, 24% strand	Q16555
B, C, D	Dihydropyrimidinase-related protein 2	protein	476	36% helix, 23% strand	Q16555

Ligands and binding sites

MG · Magnesium ion · metal · 3 copies · chains A, B, C

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	762	0.85	0.89	86	empty
2	740	0.85	0.89	77	empty
3	785	0.76	0.80	78	empty
4	744	0.75	0.80	69	empty
5	258	0.68	0.84	35	empty

Interfaces

6 interfaces between chains.

B–D · 1276 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 1248 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 1218 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1214 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 22 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2VM8 · Human CRMP-2 crystallised in the presence of Mg · 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 2VM8 · PDBe 2VM8 · UniProt Q16555

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