3WV3

Crystal structure of the catalytic domain of MMP-13 complexed with N-(3-methoxybenzyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-2-carboxamide

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004222	molecular_function	metalloendopeptidase activity
A	0006508	biological_process	proteolysis
A	0008237	molecular_function	metallopeptidase activity
A	0008270	molecular_function	zinc ion binding
A	0031012	cellular_component	extracellular matrix
B	0004222	molecular_function	metalloendopeptidase activity
B	0006508	biological_process	proteolysis
B	0008237	molecular_function	metallopeptidase activity
B	0008270	molecular_function	zinc ion binding
B	0031012	cellular_component	extracellular matrix

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 301

Chain	Residue
A	HIS222
A	HIS226
A	HIS232
A	FMT306

---

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 302

Chain	Residue
A	HIS172
A	ASP174
A	HIS187
A	HIS200

---

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA A 303

Chain	Residue
A	GLY180
A	SER182
A	LEU184
A	ASP202
A	GLU205
A	ASP179

---

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA A 304

Chain	Residue
A	ASP162
A	ASN194
A	GLY196
A	ASP198
A	HOH409
A	HOH416

---

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE NA A 305

Chain	Residue
A	ASP128
A	ASP203
A	GLU205
A	HOH501

---

site_id	AC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE FMT A 306

Chain	Residue
A	HIS222
A	GLU223
A	HIS226
A	HIS232
A	ZN301
A	HOH433
A	HOH600

---

site_id	AC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 307

Chain	Residue
A	TYR176
A	HIS187
A	ALA188
A	PHE189
A	PRO190
A	HOH611
A	HOH613

---

site_id	AC8
Number of Residues	14
Details	BINDING SITE FOR RESIDUE WLL A 308

Chain	Residue
A	LEU218
A	HIS222
A	ALA238
A	LEU239
A	PHE241
A	ILE243
A	TYR244
A	THR245
A	TYR246
A	PHE252
A	MET253
A	PRO255
A	HOH476
A	HOH636

---

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 301

Chain	Residue
B	HIS222
B	HIS226
B	HIS232
B	FMT306

---

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 302

Chain	Residue
B	HIS172
B	ASP174
B	HIS187
B	HIS200

---

site_id	BC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA B 303

Chain	Residue
B	ASP179
B	GLY180
B	SER182
B	LEU184
B	ASP202
B	GLU205

---

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA B 304

Chain	Residue
B	ASP162
B	ASN194
B	GLY196
B	ASP198
B	HOH423
B	HOH449

---

site_id	BC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE NA B 305

Chain	Residue
B	ASP128
B	ASP203
B	GLU205
B	HOH533

---

site_id	BC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE FMT B 306

Chain	Residue
B	HIS222
B	GLU223
B	HIS226
B	HIS232
B	ZN301
B	HOH464

---

site_id	BC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 307

Chain	Residue
B	TYR176
B	ALA188
B	PHE189
B	HOH566

---

site_id	BC7
Number of Residues	14
Details	BINDING SITE FOR RESIDUE WLL B 308

Chain	Residue
B	HOH587
B	LEU218
B	HIS222
B	GLU223
B	ALA238
B	LEU239
B	PHE241
B	ILE243
B	TYR244
B	THR245
B	THR247
B	PHE252
B	MET253
B	PRO255

---

Functional Information from PROSITE/UniProt

site_id	PS00142
Number of Residues	10
Details	ZINC_PROTEASE Neutral zinc metallopeptidases, zinc-binding region signature. VAAHEFGHSL

Chain	Residue	Details
A	VAL219-LEU228

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	140
Details	Region: {"description":"Interaction with TIMP2"}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	2
Details	Active site: {"evidences":[{"source":"PubMed","id":"23913860","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	24
Details	Binding site: {"evidences":[{"source":"PubMed","id":"10926524","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"10986126","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15734645","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15780611","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17196980","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17623656","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19422229","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20005097","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20726512","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22689580","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23810497","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23913860","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8969305","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	16
Details	Binding site: {"evidences":[{"source":"PubMed","id":"10926524","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"10986126","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15734645","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15780611","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17196980","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17623656","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19422229","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20005097","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20726512","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22689580","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23810497","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23913860","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	2
Details	Glycosylation: {"description":"N-linked (GlcNAc...) asparagine","evidences":[{"source":"PubMed","id":"8576151","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	2
Details	Glycosylation: {"description":"N-linked (GlcNAc...) asparagine","evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---