MolNFT v1 · #113566 · protein

NOT1 C-terminal domain in complex with NOT4

5AJD · CDC39P: “NOT1 C-terminal domain in complex with NOT4”. X-ray diffraction, 20 pockets (best druggability 0.75). MolNFT v1 #113566 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5AJD
Type: protein
Length: 3,222 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CDC39P; General negative regulator of transcription subunit 4
UniProt: N1P976, P34909
Pockets: 20 · best druggability 0.75

Structure

x-ray diffraction · 11 distinct chains · 61% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CDC39P	protein	489	62% helix, 0% strand	N1P976
B, D	General negative regulator of transcription subunit 4	protein	50	26% helix, 4% strand	P34909
C	CDC39P	protein	487	64% helix, 0% strand	N1P976
E	CDC39P	protein	496	64% helix, 0% strand	N1P976
F	General negative regulator of transcription subunit 4	protein	43	28% helix, 2% strand	P34909
G	CDC39P	protein	489	64% helix, 1% strand	N1P976
H	General negative regulator of transcription subunit 4	protein	45	36% helix, 7% strand	P34909
I	CDC39P	protein	490	63% helix, 0% strand	N1P976
J	General negative regulator of transcription subunit 4	protein	48	33% helix, 2% strand	P34909
K	CDC39P	protein	489	63% helix, 0% strand	N1P976
L	General negative regulator of transcription subunit 4	protein	46	35% helix, 2% strand	P34909

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1080	0.75	0.78	75	empty
2	1127	0.74	0.77	88	empty
3	999	0.74	0.77	94	empty
4	1046	0.73	0.76	83	empty
5	777	0.73	0.78	77	empty

Interfaces

21 interfaces between chains.

I–J · 1651 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 1537 Å² buried · 7 hydrogen bonds · protein-protein
E–F · 1517 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 1493 Å² buried · 6 hydrogen bonds · protein-protein
K–L · 1487 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5AJD · Not1 C-terminal domain in complex with Not4 · the same entry in another collection · chain L against L, 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 N1P976
Every structure of UniProt P34909
Elsewhere: RCSB PDB 5AJD · PDBe 5AJD · UniProt N1P976 · UniProt P34909

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