4XKL

Crystal structure of NDP52 ZF2 in complex with mono-ubiquitin

Functional Information from PDB Data

site_id	AC1
Number of Residues	9
Details	binding site for residue GOL A 101

Chain	Residue
A	THR7
A	LEU8
A	THR9
A	LEU69
A	VAL70
A	LEU71
A	HOH213
C	LEU71
D	HOH601

---

site_id	AC2
Number of Residues	4
Details	binding site for residue ACT B 502

Chain	Residue
B	ASP426
B	LYS427
B	ILE428
B	HOH615

---

site_id	AC3
Number of Residues	4
Details	binding site for residue ZN B 503

Chain	Residue
B	CYS422
B	CYS425
B	HIS440
B	HIS444

---

site_id	AC4
Number of Residues	8
Details	binding site for residue GOL C 101

Chain	Residue
C	THR7
C	LEU8
C	THR9
C	LEU69
C	VAL70
C	LEU71
C	HOH207
C	HOH208

---

site_id	AC5
Number of Residues	2
Details	binding site for residue ACT C 102

Chain	Residue
C	LYS11
C	THR12

---

site_id	AC6
Number of Residues	1
Details	binding site for residue ACT D 501

Chain	Residue
D	CYS419

---

site_id	AC7
Number of Residues	4
Details	binding site for residue ZN D 502

Chain	Residue
D	CYS422
D	CYS425
D	HIS440
D	HIS444

---

Functional Information from PROSITE/UniProt

site_id	PS00299
Number of Residues	26
Details	UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD

Chain	Residue	Details
A	LYS27-ASP52

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	50
Details	ZN_FING: UBZ1-type => ECO:0000255|PROSITE-ProRule:PRU01253

Chain	Residue	Details
B	CYS419-HIS444
D	CYS419-HIS444
C	ARG54
C	ARG72

---

site_id	SWS_FT_FI2
Number of Residues	8
Details	BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU01253

Chain	Residue	Details
B	CYS422
B	CYS425
B	HIS440
B	HIS444
D	CYS422
D	CYS425
D	HIS440
D	HIS444

---

site_id	SWS_FT_FI3
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163

Chain	Residue	Details
B	SER445
D	SER445

---

site_id	SWS_FT_FI4
Number of Residues	2
Details	MOD_RES: (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457

Chain	Residue	Details
C	THR66
A	THR66

---

site_id	SWS_FT_FI5
Number of Residues	2
Details	MOD_RES: ADP-ribosylglycine => ECO:0000269|PubMed:28525742

Chain	Residue	Details
A	GLY76
C	GLY76

---

site_id	SWS_FT_FI6
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603

Chain	Residue	Details
A	LYS6
C	LYS6

---

site_id	SWS_FT_FI7
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)

Chain	Residue	Details
A	GLY76
C	GLY76

---

site_id	SWS_FT_FI8
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603, ECO:0000269|PubMed:16543144

Chain	Residue	Details
C	LYS11
C	LYS48
A	LYS11
A	LYS48

---

site_id	SWS_FT_FI9
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305|PubMed:15466860

Chain	Residue	Details
A	LYS27
C	LYS27

---

site_id	SWS_FT_FI10
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:25752573, ECO:0000269|PubMed:25752577, ECO:0000269|PubMed:34239127

Chain	Residue	Details
A	LYS29
C	LYS29

---

site_id	SWS_FT_FI11
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:25752577

Chain	Residue	Details
A	LYS33
C	LYS33

---

site_id	SWS_FT_FI12
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:18719106

Chain	Residue	Details
A	LYS63
C	LYS63

---