MolNFT v1 · #57278 · protein

Crystal structure of dbja (wild type type II P21)

3A2N · Haloalkane dehalogenase: “Crystal structure of dbja (wild type type II P21)”. X-ray diffraction, 1 ligand (CL), 9 pockets (best druggability 0.71). MolNFT v1 #57278 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3A2N
Type: protein
Length: 1,193 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Haloalkane dehalogenase
EC: 3.8.1.5
UniProt: P59337
Ligands: CL
Pockets: 9 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, E	Haloalkane dehalogenase (EC 3.8.1.5)	protein	298	48% helix, 19% strand	P59337
F	Haloalkane dehalogenase (EC 3.8.1.5)	protein	299	47% helix, 20% strand	P59337

Ligands and binding sites

CL · Chloride ion · ion · 3 copies · chains A, B, F

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

Pockets

9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	848	0.71	0.77	79	empty
2	224	0.66	0.84	35	empty
3	187	0.65	0.84	35	CL
4	249	0.65	0.82	36	CL
5	198	0.64	0.83	32	CL

Interfaces

5 interfaces between chains.

E–F · 939 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 892 Å² buried · 6 hydrogen bonds · protein-protein
A–F · 287 Å² buried · 3 hydrogen bonds · protein-protein
A–E · 201 Å² buried · 4 hydrogen bonds · protein-protein
B–F · 201 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3A2N · Crystal structure of DBJA (Wild Type Type II P21) · the same entry in another collection · chain E against E, TM-score 1.00
P59337 · AlphaFold monomer V2.0 prediction for haloalkane dehalogenase (P59337) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P59337
Elsewhere: RCSB PDB 3A2N · PDBe 3A2N · UniProt P59337

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