MolNFT v1 · #173053 · protein + DNA

Atomic structure of the poxvirus transcription pre-initiation complex in the initially melted state

7AMV · DNA-directed RNA polymerase 147 kda polypeptide: “Atomic structure of the poxvirus transcription pre-initiation complex in the initially melted state”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.88).…

PDB: 7AMV
Type: protein + DNA
Length: 5,432 residues
Chains: 13
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed RNA polymerase 147 kda polypeptide; DNA-directed RNA polymerase…
EC: 2.7.7.6
UniProt: Q1PIV1, Q49PH2, Q49PG1, A4GDF1, Q49QC8, Q49PL6, Q1PIU7, Q49QI2, Q49QC6, H2DZ00, Q49QE8
Ligands: ZN, MG
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 13 distinct chains · 37% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase 147 kda polypeptide (EC 2.7.7.6)	protein	1248	41% helix, 17% strand	Q1PIV1
B	DNA-directed RNA polymerase (EC 2.7.7.6)	protein	1126	34% helix, 24% strand	Q49PH2
C	DNA-directed RNA polymerase 35 kda subunit (EC 2.7.7.6)	protein	303	37% helix, 25% strand	Q49PG1
E	DNA-directed RNA polymerase subunit (EC 2.7.7.6)	protein	184	24% helix, 31% strand	A4GDF1
F	DNA-directed RNA polymerase 19 kda subunit (EC 2.7.7.6)	protein	103	59% helix, 9% strand	Q49QC8
G	DNA-directed RNA polymerase 18 kda subunit (EC 2.7.7.6)	protein	158	9% helix, 53% strand	Q49PL6
I	Protein H4	protein	694	46% helix, 12% strand	Q1PIU7
J	DNA-directed RNA polymerase 7 kda subunit (EC 2.7.7.6)	protein	61	38% helix, 8% strand	Q49QI2
K	Etf large subunit	protein	708	24% helix, 26% strand	Q49QC6
N	Synthetic promoter DNA oligomer, non-template strand	dna	42	—	—
S	DNA-directed RNA polymerase 30 kda polypeptide (EC 2.7.7.6)	protein	126	51% helix, 1% strand	H2DZ00
T	Synthetic promoter DNA oligomer, template strand	dna	42	—	—
W	ATP-dependent helicase vetfs	protein	637	41% helix, 17% strand	Q49QE8

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B, J
MG · Magnesium ion · metal · chains A

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

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	1090	0.88	0.89	143	empty
2	1077	0.87	0.88	122	empty
3	818	0.85	0.87	96	empty
4	863	0.84	0.86	85	empty
5	473	0.83	0.91	47	empty

Interfaces

40 interfaces between chains.

A–B · 9541 Å² buried · 120 hydrogen bonds · protein-protein
B–I · 5174 Å² buried · 47 hydrogen bonds · protein-protein
A–I · 3289 Å² buried · 23 hydrogen bonds · protein-protein
K–W · 3246 Å² buried · 39 hydrogen bonds · protein-protein
A–S · 3199 Å² buried · 28 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

7AMV · Atomic structure of the poxvirus transcription pre-initiation complex in the initially… · the same entry in another collection · chain A 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 Q1PIV1
Every structure of UniProt Q49PH2
Every structure of UniProt Q49PG1
Every structure of UniProt A4GDF1
Every structure of UniProt Q49QC8
Every structure of UniProt Q49PL6
Every structure of UniProt Q1PIU7
Every structure of UniProt Q49QI2
Every structure of UniProt Q49QC6
Every structure of UniProt H2DZ00
Every structure of UniProt Q49QE8
Elsewhere: RCSB PDB 7AMV · PDBe 7AMV · UniProt Q1PIV1 · UniProt Q49PH2 · UniProt Q49PG1 · UniProt A4GDF1 · UniProt Q49QC8 · UniProt Q49PL6 · UniProt Q1PIU7 · UniProt Q49QI2 · UniProt Q49QC6 · UniProt H2DZ00 · UniProt Q49QE8

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