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Crystal structure of the large ribosomal subunit from haloarcula marismortui at 2.4 ångström resolution

Analyse Crystal structure of the large ribosomal subunit from haloarcula marismortui at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1FFK
Type: protein + RNA
Length: 6,484 residues
Chains: 29
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 23S rRNA; 5S rRNA; Ribosomal protein L2; Ribosomal protein L3; Ribosomal protein L4…
UniProt: P20276, P20279, P12735, P14124, P12743, P29198, P22450, P12737, P14123, P12733, P14119, P12734, P10970, P12732, P10972, P14116, P10971, P14121, P18138, P12736, P32410, P22452, P32411, P14135
Ligands: CD, MG, K
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 29 distinct chains · 0% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0	23S rRNA	rna	2706	—	—
9	5S rRNA	rna	122	—	—
A	Ribosomal protein L2	protein	237	0% helix, 0% strand	P20276
B	Ribosomal protein L3	protein	337	0% helix, 0% strand	P20279
C	Ribosomal protein L4	protein	246	0% helix, 0% strand	P12735
D	Ribosomal protein L5	protein	140	0% helix, 0% strand	P14124
E	Ribosomal protein L7AE	protein	118	0% helix, 0% strand	P12743
F	Ribosomal protein L10E	protein	157	0% helix, 0% strand	—
G	Ribosomal protein L13	protein	142	0% helix, 0% strand	P29198
H	Ribosomal protein L14	protein	132	0% helix, 0% strand	P22450
I	Ribosomal protein L15E	protein	194	0% helix, 0% strand	—
J	Ribosomal protein L15	protein	143	0% helix, 0% strand	P12737
K	Ribosomal protein L18	protein	186	0% helix, 0% strand	P14123
L	Ribosomal protein L18E	protein	115	0% helix, 0% strand	P12733
M	Ribosomal protein L19	protein	143	0% helix, 0% strand	P14119
N	Ribosomal protein L21E	protein	95	0% helix, 0% strand	P12734
O	Ribosomal protein L22	protein	150	0% helix, 0% strand	P10970
P	Ribosomal protein L23	protein	78	0% helix, 0% strand	P12732
Q	Ribosomal protein L24	protein	119	0% helix, 0% strand	P10972
R	Ribosomal protein L24E	protein	53	0% helix, 0% strand	P14116
S	Ribosomal protein L29	protein	65	0% helix, 0% strand	P10971
T	Ribosomal protein L30	protein	154	0% helix, 0% strand	P14121
U	Ribosomal protein L31E	protein	85	0% helix, 0% strand	P18138
V	Ribosomal protein L32E	protein	143	0% helix, 0% strand	P12736
W	Ribosomal protein L37AE	protein	73	0% helix, 0% strand	—
X	Ribosomal protein L37E	protein	56	0% helix, 0% strand	P32410
Y	Ribosomal protein L39E	protein	31	0% helix, 0% strand	P22452
Z	Ribosomal protein L44E	protein	92	0% helix, 0% strand	P32411
1	Ribosomal protein L6	protein	172	0% helix, 0% strand	P14135

Ligands and binding sites

CD · Cadmium ion · metal · 4 copies · chains R, X, W, Z
MG · Magnesium ion · metal · 2 copies · chains 0
K · Potassium ion · metal · chains 0

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	893	0.86	0.89	87	empty
2	605	0.85	0.91	78	empty
3	669	0.84	0.90	62	empty
4	616	0.84	0.90	75	empty
5	838	0.84	0.87	94	empty

Interfaces

45 interfaces between chains.

0–B · 3379 Å² buried · 0 hydrogen bonds · protein-nucleic
0–A · 3061 Å² buried · 0 hydrogen bonds · protein-nucleic
0–I · 2513 Å² buried · 0 hydrogen bonds · protein-nucleic
0–C · 2254 Å² buried · 0 hydrogen bonds · protein-nucleic
0–M · 1698 Å² buried · 0 hydrogen bonds · protein-nucleic

Compared structures

1FFK · Crystal structure of the large ribosomal subunit from haloarcula marismortui at 2.4… · the same entry in another collection · chain I against I, 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 P20276
Every structure of UniProt P20279
Every structure of UniProt P12735
Every structure of UniProt P14124
Every structure of UniProt P12743
Every structure of UniProt P29198
Every structure of UniProt P22450
Every structure of UniProt P12737
Every structure of UniProt P14123
Every structure of UniProt P12733
Every structure of UniProt P14119
Every structure of UniProt P12734
Every structure of UniProt P10970
Every structure of UniProt P12732
Every structure of UniProt P10972
Every structure of UniProt P14116
Every structure of UniProt P10971
Every structure of UniProt P14121
Every structure of UniProt P18138
Every structure of UniProt P12736
Every structure of UniProt P32410
Every structure of UniProt P22452
Every structure of UniProt P32411
Every structure of UniProt P14135
Elsewhere: RCSB PDB 1FFK · PDBe 1FFK · UniProt P20276 · UniProt P20279 · UniProt P12735 · UniProt P14124 · UniProt P12743 · UniProt P29198 · UniProt P22450 · UniProt P12737 · UniProt P14123 · UniProt P12733 · UniProt P14119 · UniProt P12734 · UniProt P10970 · UniProt P12732 · UniProt P10972 · UniProt P14116 · UniProt P10971 · UniProt P14121 · UniProt P18138 · UniProt P12736 · UniProt P32410 · UniProt P22452 · UniProt P32411 · UniProt P14135

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