General information
PDB ID 5GMK
Title CRYO-EM STRUCTURE OF THE CATALYTIC STEP I SPLICEOSOME (C COMPLEX) AT 3.4 ANGSTROM RESOLUTION
PDB header RNA BINDING PROTEIN/RNA
Date 2016-07-14
Experimental method ELECTRON MICROSCOPY
Resolution (A) 3.4
Kind rna
Organism SACCHAROMYCES CEREVISIAE S288C
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PDB PDBe MMDB Jena OCA
CATH PDBsum HSSP PDBePISA UniProt
ProteopediA BIPA WebPDA
PRIDB
Composition of PDB entry and biounits
File: Protein chains: DNA chains: RNA chains: No. of models: Action:
PDB entry:
pdb5gmk.pdb ACJOPQRSTZcdFGHIvnopqrtkihjlmgsuwxyzeab DELMBN 0
Pfam domains
Name: Type: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Action:
PROCN Domain 1.7e-218 1 No_clan A 470 874 BDELN
PRP8_domainIV Domain 9.5e-118 1 No_clan A 1824 2061 M
PRO8NT Domain 2.3e-79 1 No_clan A 131 282 DE
U5_2-snRNA_bdg Domain 3.2e-69 1 No_clan A 1282 1415 BM
RRM_4 Domain 2.5e-47 1 No_clan A 1059 1150 L
U6-snRNA_bdg Domain 2.7e-41 1 CL0363 A 1577 1672 BL
RRM_5 Domain 0.0000000082 1 CL0221 a 29 110 L
GTP_EFTU Domain 2.9e-36 1 CL0023 C 131 443 DE
GTP_EFTU_D2 Domain 3.3e-16 1 CL0575 C 481 578
EFG_C Domain 0.000000000000012 1 CL0437 C 856 948
EFG_IV Domain 0.00000000000064 1 CL0329 C 738 854
Myb_DNA-binding Domain 0.0000000000032 1 CL0123 c 10 56 LE
Myb_DNA-binding Domain 0.00000038 1 CL0123 c 63 106 D
LSM Domain 2.5e-17 1 CL0527 e 44 106 L
LSM Domain 1e-17 1 CL0527 g 37 106 D
Cir_N Domain 0.000000000036 1 No_clan G 11 42 DL
LSM Domain 2.1e-18 1 CL0527 h 17 83 DEMN
LSM Domain 2e-16 1 CL0527 i 19 92 D
SYF2 Domain 0.00000021 1 No_clan I 93 210 LE
LSM Domain 3.6e-16 1 CL0527 j 5 73 BD
LSM Domain 2.1e-22 1 CL0527 k 10 97 D
LSM Domain 2.1e-16 1 CL0527 l 9 74 D
LSM Domain 6.1e-27 1 CL0527 m 5 97 D
Prp19 Domain 5.9e-26 1 No_clan o 62 139
U-box Domain 0.0001 1 CL0229 o 1 84
Prp19 Domain 6.2e-26 1 No_clan p 62 139 DE
U-box Domain 0.00011 1 CL0229 p 1 84
Prp19 Domain 2.2e-25 1 No_clan q 59 139
Torus Domain 5e-33 1 CL0537 R 4 114 EN
Prp19 Domain 5.8e-26 1 No_clan r 62 139 EN
RRM_1 Domain 0.0000037 1 CL0221 R 149 206 EN
U-box Domain 0.00012 1 CL0229 r 1 85 EN
LSM Domain 1.9e-22 1 CL0527 s 10 97 DEL
G10 Domain 6.1e-64 1 No_clan T 1 155 DE
LSM Domain 2e-16 1 CL0527 u 19 92 L
LSM Domain 2.1e-18 1 CL0527 w 17 83 L
LSM Domain 3.6e-16 1 CL0527 x 5 73 L
LSM Domain 2.1e-16 1 CL0527 y 9 74 L
LSM Domain 6.1e-27 1 CL0527 z 5 97 L
HAT Family 0.0000012 1 CL0020 d 180 211
DUF572 Family 3.7e-42 1 No_clan F 2 116 BELM
Isy1 Family 5.7e-33 1 No_clan H 2 96 DELMN
SKIP_SNW Family 6.2e-38 1 No_clan P 88 247 DLE
Cwf_Cwc_15 Family 0.000024 0 No_clan S 4 133 DEL
Cwf_Cwc_15 Family 0.0001 0 No_clan S 126 175
BCAS2 Family 0.00026 0 No_clan t 1 175 DE
MA3 Family 5.8e-26 1 CL0020 Z 291 398
LRR_9 Repeat 0.00000065 0 CL0022 b 51 162
WD40 Repeat 0.0000011 1 CL0186 n 275 321
WD40 Repeat 0.0000019 1 CL0186 n 192 234
WD40 Repeat 0.00007 1 CL0186 n 152 191
WD40 Repeat 0.000015 1 CL0186 O 214 252 E
WD40 Repeat 0.000031 1 CL0186 O 129 168
WD40 Repeat 0.00026 1 CL0186 O 172 210
WD40 Repeat 0.00058 1 CL0186 O 256 294
SCOP domains
No SCOP domains
GO terms
No GO terms
Sequences
Download file with secondary structure created by Stride  
pdb5gmk.pdb:   [ download sequences in FASTA format ]
A (protein): 
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c (protein): 
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d (protein): 
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e (protein): 
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F (protein): 
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G (protein): 
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H (protein): 
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I (protein): 
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J (protein): 
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k (protein): 
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o (protein): 
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P (protein): 
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q (protein): 
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R (protein): 
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s (protein): 
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T (protein): 
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u (protein): 
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v (protein): 
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w (protein): 
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x (protein): 
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y (protein): 
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Z (protein): 
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B (rna): 
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L (rna): 
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M (rna): 
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N (rna): 
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