MolNFT v1 · #137869 · protein

X-ray crystal structure of escherichia COLI RNA polymerase and dksa complex

5W1T · DNA-directed RNA polymerase subunit alpha: “X-ray crystal structure of escherichia COLI RNA polymerase and dksa complex”. X-ray diffraction, 2 ligands (ZN, MG), 20 pockets (best druggability 0.83). MolNFT v1 #137869 on GenesisL1: 3D…

PDB: 5W1T
Type: protein
Length: 7,374 residues
Chains: 14
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase subunit beta…
EC: 2.7.7.6
UniProt: P0A7Z4, P0A8V2, P0A8T7, P0A800, P00579, P0ABS1
Ligands: ZN, MG
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 12 distinct chains · 41% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	319	26% helix, 24% strand	P0A7Z4
B	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	217	18% helix, 35% strand	P0A7Z4
C, I	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1340	30% helix, 23% strand	P0A8V2
D	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1171	42% helix, 14% strand	P0A8T7
E	Rpoz	protein	89	63% helix, 0% strand	P0A800
F	RNA polymerase sigma factor rpod	protein	468	63% helix, 3% strand	P00579
G	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	227	20% helix, 38% strand	P0A7Z4
H	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	216	18% helix, 36% strand	P0A7Z4
J	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1159	43% helix, 14% strand	P0A8T7
K	Rpoz	protein	79	62% helix, 0% strand	P0A800
L	RNA polymerase sigma factor rpod	protein	469	65% helix, 3% strand	P00579
M, N	RNA polymerase-binding transcription factor dksa	protein	140	69% helix, 1% strand	P0ABS1

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains D, J, M, N
MG · Magnesium ion · metal · 2 copies · chains D, J

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	565	0.83	0.89	61	empty
2	560	0.83	0.89	79	empty
3	637	0.83	0.87	62	empty
4	471	0.82	0.89	65	empty
5	391	0.82	0.91	56	empty

Interfaces

26 interfaces between chains.

I–J · 8362 Å² buried · 103 hydrogen bonds · protein-protein
C–D · 8314 Å² buried · 103 hydrogen bonds · protein-protein
J–L · 2828 Å² buried · 28 hydrogen bonds · protein-protein
D–F · 2823 Å² buried · 28 hydrogen bonds · protein-protein
A–B · 2099 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

5W1T · X-ray crystal structure of Escherichia coli RNA polymerase and DksA complex · the same entry in another collection · chain N against N, 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 P0A7Z4
Every structure of UniProt P0A8V2
Every structure of UniProt P0A8T7
Every structure of UniProt P0A800
Every structure of UniProt P00579
Every structure of UniProt P0ABS1
Elsewhere: RCSB PDB 5W1T · PDBe 5W1T · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P00579 · UniProt P0ABS1

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