MolNFT v1 · #102268 · protein

Crystal structure of P-tefb complex with AFF4 and tat

4OGR · Cyclin-dependent kinase 9: “Crystal structure of P-tefb complex with AFF4 and tat”. X-ray diffraction, 3 ligands (ACE, ADN, ZN), 20 pockets (best druggability 0.75). MolNFT v1 #102268 on GenesisL1: 3D structure, binding sites and…

PDB: 4OGR
Type: protein
Length: 2,002 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyclin-dependent kinase 9; Cyclin-T1; AF4/FMR2 family member 4; Protein tat
EC: 2.7.11.22, 2.7.11.23
UniProt: P50750, O60563, Q9UHB7, P69698
Ligands: ACE, ADN, ZN
Pockets: 20 · best druggability 0.75

Structure

x-ray diffraction · 8 distinct chains · 43% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclin-dependent kinase 9 (EC 2.7.11.22, 2.7.11.23)	protein	315	37% helix, 16% strand	P50750
B, F, K	Cyclin-T1	protein	255	65% helix, 1% strand	O60563
C	AF4/FMR2 family member 4	protein	55	47% helix, 4% strand	Q9UHB7
E	Cyclin-dependent kinase 9 (EC 2.7.11.22, 2.7.11.23)	protein	311	40% helix, 14% strand	P50750
G	AF4/FMR2 family member 4	protein	36	39% helix, 6% strand	Q9UHB7
I	Cyclin-dependent kinase 9 (EC 2.7.11.22, 2.7.11.23)	protein	319	38% helix, 16% strand	P50750
L	AF4/FMR2 family member 4	protein	54	48% helix, 4% strand	Q9UHB7
D, H, M	Protein tat	protein	49	31% helix, 2% strand	P69698

Ligands and binding sites

ACE · Acetyl group · ligand · 3 copies · chains B, D, F, H, K, M
ADN · Adenosine · ligand · 3 copies · chains A, E, I
ZN · Zinc ion · metal · 6 copies · chains D, B, H, F, M, K

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	120	0.75	0.94	25	empty
2	389	0.69	0.81	39	empty
3	75	0.69	0.93	20	empty
4	185	0.66	0.85	26	ADN
5	188	0.64	0.84	23	ADN

Interfaces

21 interfaces between chains.

F–H · 1802 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 1743 Å² buried · 15 hydrogen bonds · protein-protein
K–M · 1675 Å² buried · 14 hydrogen bonds · protein-protein
F–G · 1618 Å² buried · 25 hydrogen bonds · protein-protein
B–C · 1536 Å² buried · 26 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 covalent, 3 modified, 1 disulfide (covalent ligand, phosphorylation, disulfide).

Compared structures

4OGR · crystal structure of P-TEFb complex with AFF4 and Tat · the same entry in another collection · chain M against M, 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 P50750
Every structure of UniProt O60563
Every structure of UniProt Q9UHB7
Every structure of UniProt P69698
Elsewhere: RCSB PDB 4OGR · PDBe 4OGR · UniProt P50750 · UniProt O60563 · UniProt Q9UHB7 · UniProt P69698

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