6CIM

Pre-Reaction Complex, RAG1(E962Q)/2-nicked/intact 12/23RSS complex in Mn2+

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004519	molecular_function	endonuclease activity
A	0033151	biological_process	V(D)J recombination
A	0043565	molecular_function	sequence-specific DNA binding
A	0061630	molecular_function	ubiquitin protein ligase activity
B	0003677	molecular_function	DNA binding
B	0005634	cellular_component	nucleus
B	0006310	biological_process	DNA recombination
C	0004519	molecular_function	endonuclease activity
C	0033151	biological_process	V(D)J recombination
C	0043565	molecular_function	sequence-specific DNA binding
C	0061630	molecular_function	ubiquitin protein ligase activity
D	0003677	molecular_function	DNA binding
D	0005634	cellular_component	nucleus
D	0006310	biological_process	DNA recombination
N	0003677	molecular_function	DNA binding
N	0005634	cellular_component	nucleus

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	binding site for residue ZN A 1101

Chain	Residue
A	CYS727
A	CYS730
A	HIS937
A	HIS942

---

site_id	AC2
Number of Residues	2
Details	binding site for residue MN A 1102

Chain	Residue
A	ASP600
A	ASP708

---

site_id	AC3
Number of Residues	4
Details	binding site for residue ZN C 1101

Chain	Residue
C	HIS942
C	CYS727
C	CYS730
C	HIS937

---

site_id	AC4
Number of Residues	3
Details	binding site for residue MN C 1102

Chain	Residue
C	ASP600
C	GLU662
C	ASP708

---

Functional Information from PROSITE/UniProt

site_id	PS00353
Number of Residues	12
Details	HMG_BOX_1 HMG box A DNA-binding domain signature. FSKKCsERWKTM

Chain	Residue	Details
N	PHE41-MET52

---

site_id	PS00435
Number of Residues	11
Details	PEROXIDASE_1 Peroxidases proximal heme-ligand signature. DTVYILGGHSL

Chain	Residue	Details
B	ASP214-LEU224

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	70
Details	DNA_BIND: HMG box 1 => ECO:0000255|PROSITE-ProRule:PRU00267

Chain	Residue	Details
N	PRO9-ILE79
C	GLY389-GLN456

---

site_id	SWS_FT_FI2
Number of Residues	68
Details	DNA_BIND: HMG box 2 => ECO:0000255|PROSITE-ProRule:PRU00267

Chain	Residue	Details
N	PRO95-ARG163
A	ASP708
A	GLN962
C	ASP600
C	ASP708
C	GLN962

---

site_id	SWS_FT_FI3
Number of Residues	1
Details	BINDING: BINDING => ECO:0000250|UniProtKB:P10103

Chain	Residue	Details
N	MET1
C	TRP893

---

site_id	SWS_FT_FI4
Number of Residues	1
Details	SITE: Cleavage; by thrombin:thrombomodulin => ECO:0000250|UniProtKB:P10103

Chain	Residue	Details
N	ARG10

---

site_id	SWS_FT_FI5
Number of Residues	1
Details	SITE: Cleavage; by CASP1 => ECO:0000269|PubMed:24474694

Chain	Residue	Details
N	ASP67

---

site_id	SWS_FT_FI6
Number of Residues	8
Details	MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:P10103

Chain	Residue	Details
N	LYS3
N	LYS7
N	LYS8
N	LYS12
N	LYS28
N	LYS29
N	LYS127
N	LYS128

---

site_id	SWS_FT_FI7
Number of Residues	2
Details	MOD_RES: Cysteine sulfonic acid (-SO3H); alternate => ECO:0000250|UniProtKB:P63159

Chain	Residue	Details
N	CYS23
N	CYS45

---

site_id	SWS_FT_FI8
Number of Residues	1
Details	MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861

Chain	Residue	Details
N	LYS30

---

site_id	SWS_FT_FI9
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163

Chain	Residue	Details
N	SER35

---

site_id	SWS_FT_FI10
Number of Residues	3
Details	MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:P63158

Chain	Residue	Details
N	LYS43
N	LYS90
N	LYS141

---

site_id	SWS_FT_FI11
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648

Chain	Residue	Details
N	SER100

---

site_id	SWS_FT_FI12
Number of Residues	1
Details	MOD_RES: Cysteine sulfonic acid (-SO3H) => ECO:0000250|UniProtKB:P63159

Chain	Residue	Details
N	CYS106

---

site_id	SWS_FT_FI13
Number of Residues	5
Details	CROSSLNK: Isoglutamyl lysine isopeptide (Lys-Gln) (interchain with Q-?) => ECO:0000269|PubMed:29618516

Chain	Residue	Details
N	LYS28
N	LYS43
N	LYS44
N	LYS68

---