eF-site ID 6a6j-ABCD
PDB Code 6a6j
Chain A, B, C, D

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Title Crystal structure of Zebra fish Y-box protein1 (YB-1) Cold-shock domain in complex with 6mer m5C RNA
Classification RNA BINDING PROTEIN/RNA
Compound Zebra fish Y-box protein1 (YB-1)
Source (6A6J)
Sequence A:  KVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIK
KNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGPGGVP
VQGSKYAADR
B:  CAUXU
C:  KVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIK
KNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGPGGVP
VQGSKYAADR
D:  CAUXU
Description


Functional site
1) chain A
residue 97
type
sequence E
description binding site for residue ZN A 201
source : AC1
2) chain A
residue 101
type
sequence E
description binding site for residue ZN A 201
source : AC1
3) chain B
residue 2
type
sequence C
description binding site for residue ZN A 201
source : AC1
4) chain C
residue 97
type
sequence E
description binding site for residue ZN C 201
source : AC2
5) chain C
residue 101
type
sequence E
description binding site for residue ZN C 201
source : AC2
6) chain D
residue 2
type
sequence C
description binding site for residue ZN C 201
source : AC2
7) chain A
residue 52-71
type prosite
sequence YGFINRNDTKEDVFVHQTAI
description CSD_1 Cold-shock (CSD) domain signature. YGFInrndtkeDVFvHqTaI
source prosite : PS00352
8) chain A
residue 45
type SITE
sequence W
description Important for C5-methylcytosine-recognition => ECO:0000269|PubMed:31358969
source Swiss-Prot : SWS_FT_FI1
9) chain C
residue 45
type SITE
sequence W
description Important for C5-methylcytosine-recognition => ECO:0000269|PubMed:31358969
source Swiss-Prot : SWS_FT_FI1
10) chain A
residue 82
type MOD_RES
sequence S
description Phosphoserine; by PKB/AKT1 => ECO:0000269|PubMed:15806160, ECO:0007744|PubMed:19690332
source Swiss-Prot : SWS_FT_FI2
11) chain C
residue 82
type MOD_RES
sequence S
description Phosphoserine; by PKB/AKT1 => ECO:0000269|PubMed:15806160, ECO:0007744|PubMed:19690332
source Swiss-Prot : SWS_FT_FI2
12) chain C
residue 117
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:18851979
source Swiss-Prot : SWS_FT_FI3
13) chain A
residue 117
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:18851979
source Swiss-Prot : SWS_FT_FI3

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