Research workbench

Giardia Ribosome in PRE-T Classical State (C)

Analyse Giardia Ribosome in PRE-T Classical State (C) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8BSJ
Type: protein + RNA
Length: 14,728 residues
Chains: 79
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 6.49
Source: Giardia intestinalis
Molecule: Ribosomal protein L2; Ribosomal protein L3; Ribosomal protein L4; 5.8S rRNA; 5S rRNA…
UniProt: E2RTN4, A8BRZ3, A8B7H8, E2RU47, A0A644EZB9, A8BRY6, A8BLL7, A8BNT5, A8BM86, A8BI95, A8B6M8, A8B4F8, A8B8Z6, A8BU75, A8BE76, A8B4T7, A8BH61, A8BT04, A8B2Q4, A0A644FC41, A8BS37, A8B7P2, A8BMP6, A8BFT3, A8B1T3, A8BZ78, A8BYY2, A8B5N7, A8BMP3, A8BMD9, A8BKK5, A8BMF7, A0A644FBK5, A8BYA6, A8BLV7, A8B481, A0A644FB74, V6TX21, A8BQU8, A8BN26, A8BXE1, A0A644FB17, A8BMZ1, A8B8Z2, A0A644F9A2, A8BFE3, A8BZD3, A8B6L8, A8BT38, A8B252, E2RU77, A8BKS8, A8BRX3, A8BVU0, V6T9I6, A8BE02, Q76KS3, A8BBP3, A8BKC6, A8BRG5, A8BZ58, A0A644F964, A8B4G0, A8B484, A8B593, A8B8H7, A8BQZ7, A0A644F5K9, A8B4F3, A8B7H6, A0A644F843
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · resolution 6.49 · 78 distinct chains · 31% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
LA	Ribosomal protein L2	protein	243	8% helix, 24% strand	E2RTN4
LB	Ribosomal protein L3	protein	374	14% helix, 28% strand	A8BRZ3
LC	Ribosomal protein L4	protein	309	34% helix, 8% strand	A8B7H8
LD	5.8S rRNA	rna	140	—	—
LE	5S rRNA	rna	116	—	—
LF	Ribosomal protein L5	protein	289	43% helix, 9% strand	E2RU47
LG	Ribosomal protein L39	protein	50	36% helix, 0% strand	A0A644EZB9
LH	Ribosomal protein L7	protein	217	50% helix, 13% strand	A8BRY6
LI	60S ribosomal protein L7a	protein	183	51% helix, 8% strand	A8BLL7
LJ	Ribosomal protein L6	protein	184	19% helix, 33% strand	A8BNT5
LK	Ribosomal protein L10	protein	197	22% helix, 23% strand	A8BM86
LL	Ribosomal protein L11	protein	165	25% helix, 22% strand	A8BI95
LM	60S ribosomal protein L13	protein	195	44% helix, 8% strand	A8B6M8
LN	Ribosomal protein L14	protein	126	41% helix, 25% strand	A8B4F8
LO	Ribosomal protein L15	protein	201	35% helix, 16% strand	A8B8Z6
LP	Ribosomal protein L13a	protein	189	47% helix, 11% strand	A8BU75
LQ	Ribosomal protein L17	protein	153	33% helix, 24% strand	A8BE76
LR	Ribosomal protein L18	protein	178	29% helix, 11% strand	A8B4T7
LS	Ribosomal protein L19	protein	187	68% helix, 3% strand	A8BH61
LT	60S ribosomal protein L18a	protein	170	29% helix, 31% strand	A8BT04
LU	Ribosomal protein L21	protein	150	19% helix, 26% strand	A8B2Q4
LV	Ribosomal L22e	protein	105	26% helix, 16% strand	A0A644FC41
LW	Ribosomal protein L23	protein	132	11% helix, 35% strand	A8BS37
LX	Ribosomal protein L24	protein	60	25% helix, 13% strand	A8B7P2
LY	Ribosomal protein L23A	protein	113	30% helix, 23% strand	A8BMP6
LZ	Ribosomal protein L26	protein	133	32% helix, 28% strand	A8BFT3
La	60S ribosomal protein L27	protein	121	17% helix, 25% strand	A8B1T3
Lb	Ribosomal protein L27a	protein	145	32% helix, 12% strand	A8BZ78
Lc	60S ribosomal protein L29	protein	55	42% helix, 2% strand	A8BYY2
Ld	Ribosomal protein L30	protein	98	45% helix, 13% strand	A8B5N7
Le	Ribosomal protein L31B	protein	97	31% helix, 20% strand	A8BMP3
Lf	Ribosomal protein L32	protein	125	19% helix, 9% strand	A8BMD9
Lg	Ribosomal protein L35a	protein	98	0% helix, 46% strand	A8BKK5
Lh	Ribosomal protein L34	protein	104	21% helix, 13% strand	A8BMF7
Li	Ribosomal protein L29	protein	118	64% helix, 3% strand	A0A644FBK5
Lj	Ribosomal protein L36-1	protein	84	61% helix, 0% strand	A8BYA6
Lk	Ribosomal protein L37	protein	85	32% helix, 11% strand	A8BLV7
Ll	Ribosomal L38e	protein	72	24% helix, 31% strand	A8B481
Ln	Ribosomal protein L10a	protein	200	36% helix, 13% strand	A0A644FB74
Lo	60S ribosomal protein L41	protein	25	88% helix, 0% strand	V6TX21
Lp	Ribosomal protein L44	protein	91	11% helix, 27% strand	A8BQU8
Lq	Ribosomal protein L37a	protein	91	38% helix, 14% strand	A8BN26
Ls	Ubiquitin/Ribosomal protein L40e	protein	47	17% helix, 13% strand	A8BXE1
Lt	Large Subunit rRNA	rna	2593	—	—
SA	40S ribosomal protein SA	protein	194	38% helix, 12% strand	A0A644FB17
SB	Ribosomal protein S2	protein	213	29% helix, 28% strand	A8BMZ1
SC	Ribosomal protein S3	protein	206	33% helix, 17% strand	A8B8Z2
SD	40S ribosomal protein S3a	protein	228	27% helix, 32% strand	A0A644F9A2
SE	40S ribosomal protein S4	protein	260	13% helix, 29% strand	A8BFE3
SF	Ribosomal protein S5	protein	179	54% helix, 4% strand	A8BZD3
SG	40S ribosomal protein S6	protein	224	25% helix, 17% strand	A8B6L8
SH	40S ribosomal protein S7	protein	184	29% helix, 10% strand	A8BT38
SI	40S ribosomal protein S8	protein	167	18% helix, 21% strand	A8B252
SJ	Ribosomal protein S15A	protein	129	30% helix, 26% strand	E2RU77
SK	Ribosomal protein S9	protein	172	49% helix, 2% strand	A8BKS8
SL	Ribosomal protein S10B	protein	109	32% helix, 6% strand	A8BRX3
SM	Ribosomal protein S11	protein	147	5% helix, 29% strand	A8BVU0
SO	SSU ribosomal protein S12P	protein	140	24% helix, 29% strand	V6T9I6
SP	Ribosomal protein S13	protein	150	55% helix, 0% strand	A8BE02
SQ	Ribosomal protein S14	protein	124	23% helix, 22% strand	Q76KS3
SR	Ribosomal protein S15	protein	113	27% helix, 14% strand	A8BBP3
ST	Ribosomal protein S16	protein	151	34% helix, 13% strand	A8BKC6
SU	Ribosomal protein S17	protein	121	47% helix, 2% strand	A8BRG5
SV	Ribosomal protein S18	protein	142	30% helix, 6% strand	A8BZ58
SW	Ribosomal protein S19e	protein	138	46% helix, 7% strand	A0A644F964
SX	Ribosomal protein S20	protein	107	25% helix, 40% strand	A8B4G0
SY	40S ribosomal protein S21	protein	85	21% helix, 14% strand	A8B484
Sb	Ribosomal protein S24	protein	120	31% helix, 27% strand	A8B593
Sc	40S ribosomal protein S25	protein	75	36% helix, 8% strand	A8B8H7
Sd	40S ribosomal protein S26	protein	97	23% helix, 21% strand	A8BQZ7
Se	Ribosomal protein S27	protein	80	8% helix, 18% strand	A0A644F5K9
Sg	Ribosomal protein S28	protein	61	0% helix, 41% strand	A8B4F3
Sh	Ribosomal protein S29A	protein	48	19% helix, 2% strand	A8B7H6
Sj	40S ribosomal protein S30	protein	67	31% helix, 3% strand	A0A644F843
St	Small Subunit rRNA	rna	1454	—	—
u, v	tRNA	rna	75	—	—
x	tRNA	rna	74	—	—
y	mRNA	rna	11	—	—

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	885	0.89	0.93	88	empty
2	1144	0.89	0.91	128	empty
3	1016	0.89	0.90	107	empty
4	1000	0.89	0.91	86	empty
5	1017	0.88	0.91	83	empty

Interfaces

253 interfaces between chains.

LB–Lt · 8540 Å² buried · 211 hydrogen bonds · protein-nucleic
LO–Lt · 7169 Å² buried · 154 hydrogen bonds · protein-nucleic
LA–Lt · 6722 Å² buried · 183 hydrogen bonds · protein-nucleic
LC–Lt · 6387 Å² buried · 151 hydrogen bonds · protein-nucleic
Lb–Lt · 5031 Å² buried · 123 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 34 disulfide (disulfide).

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