MolNFT v1 · #37789 · protein

Crystal structure of the POB3 middle domain

2GCJ · Hypothetical 63.0 kda protein in DAK1-ORC1 intergenic region: “Crystal structure of the POB3 middle domain”. X-ray diffraction, 11 pockets (best druggability 0.74). MolNFT v1 #37789 on GenesisL1: 3D structure, binding sites and…

PDB: 2GCJ
Type: protein
Length: 919 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical 63.0 kda protein in DAK1-ORC1 intergenic region
UniProt: Q04636
Pockets: 11 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Hypothetical 63.0 kda protein in DAK1-ORC1 intergenic region	protein	229	18% helix, 52% strand	Q04636
B	Hypothetical 63.0 kda protein in DAK1-ORC1 intergenic region	protein	230	17% helix, 52% strand	Q04636
C	Hypothetical 63.0 kda protein in DAK1-ORC1 intergenic region	protein	231	16% helix, 52% strand	Q04636

Pockets

11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	826	0.74	0.78	79	empty
2	69	0.53	0.86	21	empty
3	122	0.51	0.81	24	empty
4	113	0.45	0.78	29	empty
5	94	0.39	0.76	19	empty

Interfaces

5 interfaces between chains.

B–C · 817 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 656 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 536 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 130 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 12 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2GCJ · Crystal Structure of the Pob3 middle domain · the same entry in another collection · chain A against A, TM-score 1.00
Q04636 · AlphaFold monomer V2.0 prediction for fact complex subunit POB3 (Q04636) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 Q04636
Elsewhere: RCSB PDB 2GCJ · PDBe 2GCJ · UniProt Q04636

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