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Crystal structure of P23-45 GP39 (6-132) bound to thermus thermophilus RNA polymerase beta-flap domain

Analyse Crystal structure of P23-45 GP39 (6-132) bound to thermus thermophilus RNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3WOF
Type: protein
Length: 2,761 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed RNA polymerase subunit beta; Putative uncharacterized protein
EC: 2.7.7.6
UniProt: Q8RQE9, A7XX65
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 8 distinct chains · 9% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	129	10% helix, 36% strand	Q8RQE9
B, H, J, L, P, R, T, V, X	Putative uncharacterized protein	protein	102	8% helix, 43% strand	A7XX65
D, F, N	Putative uncharacterized protein	protein	103	9% helix, 43% strand	A7XX65
E, Q	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	127	10% helix, 39% strand	Q8RQE9
G, I, O, S, W	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	129	9% helix, 39% strand	Q8RQE9
K	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	128	11% helix, 38% strand	Q8RQE9
M	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	128	8% helix, 39% strand	Q8RQE9
U	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	121	10% helix, 34% strand	Q8RQE9

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	938	0.79	0.81	112	empty
2	1134	0.79	0.81	122	empty
3	755	0.75	0.80	104	empty
4	566	0.73	0.81	58	empty
5	500	0.72	0.81	68	empty

Interfaces

68 interfaces between chains.

Q–R · 1252 Å² buried · 32 hydrogen bonds · protein-protein
E–F · 1216 Å² buried · 26 hydrogen bonds · protein-protein
U–V · 1194 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 1166 Å² buried · 26 hydrogen bonds · protein-protein
O–P · 1159 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

3WOF · Crystal structure of P23-45 gp39 (6-132) bound to Thermus thermophilus RNA polymerase… · the same entry in another collection · chain E against E, 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 Q8RQE9
Every structure of UniProt A7XX65
Elsewhere: RCSB PDB 3WOF · PDBe 3WOF · UniProt Q8RQE9 · UniProt A7XX65

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