2P82 - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CYSTEINE PROTEASE ATG4A

Authors :   J. R. Walker, T. Davis, S. Mujib, C. Butler-Cole, P. J. Finerty Jr. , J. W M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Pa Structural Genomics Consortium (Sgc)

Date :   21 Mar 07 (Deposition) - 10 Apr 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Autophagy, Hydrolase, Protease, Protein Transport, Thiol Protease, Transport, Ubl Conjugation Pathway, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. R. Walker, T. Davis, S. Mujib, C. Butler-Cole, P. J. Finerty Jr. , J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Paganon
Human Cysteine Protease Atg4A
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - CYSTEINE PROTEASE ATG4A
	Chains	:	A, B, C, D
	EC Number	:	3.4.22.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28A-LIC-TEV
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	ATG4A, APG4A, AUTL2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	AUTOPHAGY-RELATED PROTEIN 4 HOMOLOG A, HAPG4A, AUTOPHAGIN-2, AUTOPHAGY-RELATED CYSTEINE ENDOPEPTIDASE 2, AUT-LIKE 2 CYSTEINE ENDOPEPTIDASE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 16)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	EDO	15	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 1 (1, 7)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	7	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 2 (1, 8)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	8	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG D:59	BINDING SITE FOR RESIDUE CL D 1
02	AC2	SOFTWARE	ARG A:230 , TYR A:240 , MET A:348 , HOH A:604	BINDING SITE FOR RESIDUE EDO A 2
03	AC3	SOFTWARE	ASN B:175 , ARG B:230 , LEU B:231 , TYR B:240 , ARG B:347 , MET B:348 , HOH B:399	BINDING SITE FOR RESIDUE EDO B 3
04	AC4	SOFTWARE	LEU D:229 , LEU D:231 , TYR D:240 , ARG D:347 , MET D:348 , HOH D:371	BINDING SITE FOR RESIDUE EDO D 4
05	AC5	SOFTWARE	GLN A:88 , CYS A:92 , ARG A:97 , PRO A:251 , GLN A:252 , SER A:253 , HOH A:569	BINDING SITE FOR RESIDUE EDO A 360
06	AC6	SOFTWARE	LEU B:32 , GLN B:88 , CYS B:92 , PRO B:251 , SER B:253 , LEU B:254 , HOH B:532	BINDING SITE FOR RESIDUE EDO B 360
07	AC7	SOFTWARE	LEU C:32 , GLN C:88 , CYS C:92 , ARG C:97 , PRO C:251 , GLN C:252 , SER C:253 , HOH C:508	BINDING SITE FOR RESIDUE EDO C 360
08	AC8	SOFTWARE	LEU D:32 , GLN D:88 , CYS D:92 , ARG D:97 , PRO D:251 , GLN D:252 , SER D:253 , LEU D:254 , HOH D:450	BINDING SITE FOR RESIDUE EDO D 360
09	AC9	SOFTWARE	GLN D:252 , PHE D:323 , CYS D:324 , LYS D:325 , ASP D:329	BINDING SITE FOR RESIDUE EDO D 361
10	BC1	SOFTWARE	TRP A:54 , HIS A:301 , LEU A:303 , GLN A:304 , HOH A:389 , GLN C:307 , ARG C:308	BINDING SITE FOR RESIDUE EDO A 361
11	BC2	SOFTWARE	TRP B:145 , PRO B:148 , PRO B:261 , ASP B:315 , HOH B:453 , HOH B:504	BINDING SITE FOR RESIDUE EDO B 361
12	BC3	SOFTWARE	TRP A:101 , GLN A:104 , GLN A:107 , HOH A:489 , ASN C:263 , HOH C:501	BINDING SITE FOR RESIDUE EDO A 362
13	BC4	SOFTWARE	TRP C:145 , PRO C:148 , PRO C:261 , ASP C:315 , HOH C:396 , HOH C:462	BINDING SITE FOR RESIDUE EDO C 361
14	BC5	SOFTWARE	LEU C:229 , TYR C:240 , ARG C:347 , MET C:348 , HOH C:406	BINDING SITE FOR RESIDUE EDO C 362
15	BC6	SOFTWARE	LYS C:156 , LEU C:160 , ALA C:168 , VAL C:169 , MET C:185 , HOH C:445 , HOH C:452	BINDING SITE FOR RESIDUE EDO C 363
16	BC7	SOFTWARE	TRP D:145 , PRO D:148 , PRO D:261 , ASP D:315 , HOH D:365 , HOH D:459	BINDING SITE FOR RESIDUE EDO D 362

(no "SS Bond" information available for 2P82)

(no "Cis Peptide Bond" information available for 2P82)

(no "SAP(SNP)/Variant" information available for 2P82)

(no "PROSITE Motif" information available for 2P82)

Asymmetric Unit (11, 44)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000372232	1a	ENSE00001837761	X:107334898-107335066	169	ATG4A_HUMAN	1-4	4	0	-	-
1.2	ENST00000372232	2	ENSE00001642643	X:107369307-107369417	111	ATG4A_HUMAN	4-41	38	4	A:26-41 B:25-41 C:25-41 D:26-41	16 17 17 16
1.4	ENST00000372232	4	ENSE00001713101	X:107372011-107372082	72	ATG4A_HUMAN	41-65	25	4	A:41-65 B:41-65 C:41-65 D:41-65	25 25 25 25
1.5	ENST00000372232	5	ENSE00001652224	X:107374490-107374588	99	ATG4A_HUMAN	65-98	34	4	A:65-98 B:65-98 C:65-98 D:65-98	34 34 34 34
1.6	ENST00000372232	6	ENSE00001771808	X:107377287-107377388	102	ATG4A_HUMAN	98-132	35	4	A:98-132 B:98-132 C:98-132 (gaps) D:98-132 (gaps)	35 35 35 35
1.7	ENST00000372232	7	ENSE00001796296	X:107377569-107377641	73	ATG4A_HUMAN	132-156	25	4	A:132-156 B:132-156 C:132-156 D:132-156	25 25 25 25
1.8	ENST00000372232	8	ENSE00001651608	X:107380321-107380400	80	ATG4A_HUMAN	156-183	28	4	A:156-183 B:156-183 C:156-183 D:156-183	28 28 28 28
1.9b	ENST00000372232	9b	ENSE00001779238	X:107381034-107381221	188	ATG4A_HUMAN	183-245	63	4	A:183-245 (gaps) B:183-245 (gaps) C:183-245 (gaps) D:183-245 (gaps)	63 63 63 63
1.10	ENST00000372232	10	ENSE00001644003	X:107381343-107381421	79	ATG4A_HUMAN	246-272	27	4	A:246-272 B:246-272 C:246-272 D:246-272	27 27 27 27
1.11d	ENST00000372232	11d	ENSE00001776484	X:107393382-107393527	146	ATG4A_HUMAN	272-320	49	4	A:272-320 B:272-320 C:272-320 D:272-320	49 49 49 49
1.12a	ENST00000372232	12a	ENSE00002155558	X:107395032-107395088	57	ATG4A_HUMAN	321-339	19	4	A:321-339 B:321-339 C:321-339 D:321-339	19 19 19 19
1.13b	ENST00000372232	13b	ENSE00001690116	X:107396209-107396317	109	ATG4A_HUMAN	340-376	37	4	A:340-359 B:340-359 C:340-359 D:340-357	20 20 20 18
1.14c	ENST00000372232	14c	ENSE00001891122	X:107396872-107397901	1030	ATG4A_HUMAN	376-398	23	0	-	-

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:312
 aligned with ATG4A_HUMAN | Q8WYN0 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:334
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355    
          ATG4A_HUMAN    26 DELVWILGKQHLLKTEKSKLLSDISARLWFTYRRKFSPIGGTGPSSDAGWGCMLRCGQMMLAQALICRHLGRDWSWEKQKEQPKEYQRILQCFLDRKDCCYSIHQMAQMGVGEGKSIGEWFGPNTVAQVLKKLALFDEWNSLAVYVSMDNTVVIEDIKKMCRVLPLSADTAGDRPPDSLTASNQSKGTSAYCSAWKPLLLIVPLRLGINQINPVYVDAFKECFKMPQSLGALGGKPNNAYYFIGFLGDELIFLDPHTTQTFVDTEENGTVNDQTFHCLQSPQRMNILNLDPSVALGFFCKEEKDFDNWCSLVQKEILKENLRMFELVQKHPSHW 359
               SCOP domains d2p82a1 A:26-359 Cysteine protease ATG4A                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee...hhhhhhhhhhh.....eee................hhhhhhhhhhhhhhhhhhhh.............hhhhhhhhh.........hhhhhhhhhhh.........hhhhhhhhhhhhhh.......eeee....eeehhhhhhhhee.....----------------------...ee..eeeeeeee......hhhhhhhhhhhhhh..eeeeeeee..eeeeeeeee..eeeee....eee...........hhhhh.....eeee.hhh..eeeeeeee.hhhhhhhhhhhhhhhh........eee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2        -----------------------Exon 1.5  PDB: A:65-98            ---------------------------------Exon 1.7  PDB: A:132-156 --------------------------Exon 1.9b  PDB: A:183-245 (gaps) UniProt: 183-245              Exon 1.10  PDB: A:246-272  ------------------------------------------------Exon 1.12a         Exon 1.13b           Transcript 1 (1)
           Transcript 1 (2) ---------------Exon 1.4  PDB: A:41-65   --------------------------------Exon 1.6  PDB: A:98-132            -----------------------Exon 1.8  PDB: A:156-183    ----------------------------------------------------------------------------------------Exon 1.11d  PDB: A:272-320 UniProt: 272-320      --------------------------------------- Transcript 1 (2)
                 2p82 A  26 DELVWILGKQHLLKTEKSKLLSDISARLWFTYRRKFSPIGGTGPSSDAGWGCMLRCGQMMLAQALICRHLGRDWSWEKQKEQPKEYQRILQCFLDRKDCCYSIHQMAQMGVGEGKSIGEWFGPNTVAQVLKKLALFDEWNSLAVYVSMDNTVVIEDIKKMCRVLPLSA----------------------YCSAWKPLLLIVPLRLGINQINPVYVDAFKECFKMPQSLGALGGKPNNAYYFIGFLGDELIFLDPHTTQTFVDTEENGTVNDQTFHCLQSPQRMNILNLDPSVALGFFCKEEKDFDNWCSLVQKEILKENLRMFELVQKHPSHW 359
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       | -         -         -|      225       235       245       255       265       275       285       295       305       315       325       335       345       355    
                                                                                                                                                                                                 193                    216

Chain B from PDB  Type:PROTEIN  Length:312
 aligned with ATG4A_HUMAN | Q8WYN0 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:335
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354     
          ATG4A_HUMAN    25 TDELVWILGKQHLLKTEKSKLLSDISARLWFTYRRKFSPIGGTGPSSDAGWGCMLRCGQMMLAQALICRHLGRDWSWEKQKEQPKEYQRILQCFLDRKDCCYSIHQMAQMGVGEGKSIGEWFGPNTVAQVLKKLALFDEWNSLAVYVSMDNTVVIEDIKKMCRVLPLSADTAGDRPPDSLTASNQSKGTSAYCSAWKPLLLIVPLRLGINQINPVYVDAFKECFKMPQSLGALGGKPNNAYYFIGFLGDELIFLDPHTTQTFVDTEENGTVNDQTFHCLQSPQRMNILNLDPSVALGFFCKEEKDFDNWCSLVQKEILKENLRMFELVQKHPSHW 359
               SCOP domains d2p82b_ B: Cysteine protease ATG4A                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee...hhhhhhhhhhh......ee................hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhh.........hhhhhhhhhhhh........hhhhhhhhhhhhhhhh.....eeee....eeehhhhhhhhee.....-----------------------..ee..eeeeeeee......hhhhhhhhhhhhhh..eeeeeeee..eeeeeeeee..eeeee.....ee...........hhhhh.....eeee.hhh..eeeeeeee.hhhhhhhhhhhhhhhh........eee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2         -----------------------Exon 1.5  PDB: B:65-98            ---------------------------------Exon 1.7  PDB: B:132-156 --------------------------Exon 1.9b  PDB: B:183-245 (gaps) UniProt: 183-245              Exon 1.10  PDB: B:246-272  ------------------------------------------------Exon 1.12a         Exon 1.13b           Transcript 1 (1)
           Transcript 1 (2) ----------------Exon 1.4  PDB: B:41-65   --------------------------------Exon 1.6  PDB: B:98-132            -----------------------Exon 1.8  PDB: B:156-183    ----------------------------------------------------------------------------------------Exon 1.11d  PDB: B:272-320 UniProt: 272-320      --------------------------------------- Transcript 1 (2)
                 2p82 B  25 TDELVWILGKQHLLKTEKSKLLSDISARLWFTYRRKFSPIGGTGPSSDAGWGCMLRCGQMMLAQALICRHLGRDWSWEKQKEQPKEYQRILQCFLDRKDCCYSIHQMAQMGVGEGKSIGEWFGPNTVAQVLKKLALFDEWNSLAVYVSMDNTVVIEDIKKMCRVLPLSA-----------------------CSAWKPLLLIVPLRLGINQINPVYVDAFKECFKMPQSLGALGGKPNNAYYFIGFLGDELIFLDPHTTQTFVDTEENGTVNDQTFHCLQSPQRMNILNLDPSVALGFFCKEEKDFDNWCSLVQKEILKENLRMFELVQKHPSHW 359
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184        |-         -         -  |    224       234       244       254       264       274       284       294       304       314       324       334       344       354     
                                                                                                                                                                                                  193                     217

Chain C from PDB  Type:PROTEIN  Length:307
 aligned with ATG4A_HUMAN | Q8WYN0 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:335
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354     
          ATG4A_HUMAN    25 TDELVWILGKQHLLKTEKSKLLSDISARLWFTYRRKFSPIGGTGPSSDAGWGCMLRCGQMMLAQALICRHLGRDWSWEKQKEQPKEYQRILQCFLDRKDCCYSIHQMAQMGVGEGKSIGEWFGPNTVAQVLKKLALFDEWNSLAVYVSMDNTVVIEDIKKMCRVLPLSADTAGDRPPDSLTASNQSKGTSAYCSAWKPLLLIVPLRLGINQINPVYVDAFKECFKMPQSLGALGGKPNNAYYFIGFLGDELIFLDPHTTQTFVDTEENGTVNDQTFHCLQSPQRMNILNLDPSVALGFFCKEEKDFDNWCSLVQKEILKENLRMFELVQKHPSHW 359
               SCOP domains d2p82c_ C: Cysteine protease ATG4A                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee...hhhhhhhhhhhh.....ee................hhhhhhhhhhhhhhhhhhhhh.....---...hhhhhhhhhh.........hhhhhhhhhhh.........hhhhhhhhhhhhhhhh.....eeee....eeehhhhhhhhee....-------------------------.ee..eeeeeeee......hhhhhhhhhhhhhh..eeeeeeee..eeeeeeeee..eeeee.....ee...........hhhhh.....eeee.hhh..eeeeeeee.hhhhhhhhhhhhhhhh........eee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2         -----------------------Exon 1.5  PDB: C:65-98            ---------------------------------Exon 1.7  PDB: C:132-156 --------------------------Exon 1.9b  PDB: C:183-245 (gaps) UniProt: 183-245              Exon 1.10  PDB: C:246-272  ------------------------------------------------Exon 1.12a         Exon 1.13b           Transcript 1 (1)
           Transcript 1 (2) ----------------Exon 1.4  PDB: C:41-65   --------------------------------Exon 1.6  PDB: C:98-132 (gaps)     -----------------------Exon 1.8  PDB: C:156-183    ----------------------------------------------------------------------------------------Exon 1.11d  PDB: C:272-320 UniProt: 272-320      --------------------------------------- Transcript 1 (2)
                 2p82 C  25 TDELVWILGKQHLLKTEKSKLLSDISARLWFTYRRKFSPIGGTGPSSDAGWGCMLRCGQMMLAQALICRHLGRDWSW---KEQPKEYQRILQCFLDRKDCCYSIHQMAQMGVGEGKSIGEWFGPNTVAQVLKKLALFDEWNSLAVYVSMDNTVVIEDIKKMCRVLPLS-------------------------SAWKPLLLIVPLRLGINQINPVYVDAFKECFKMPQSLGALGGKPNNAYYFIGFLGDELIFLDPHTTQTFVDTEENGTVNDQTFHCLQSPQRMNILNLDPSVALGFFCKEEKDFDNWCSLVQKEILKENLRMFELVQKHPSHW 359
                                    34        44        54        64        74        84        94      |  -|      114       124       134       144       154       164       174       184       | -         -         -   |   224       234       244       254       264       274       284       294       304       314       324       334       344       354     
                                                                                                      101 105                                                                                    192                       218

Chain D from PDB  Type:PROTEIN  Length:301
 aligned with ATG4A_HUMAN | Q8WYN0 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:332
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355  
          ATG4A_HUMAN    26 DELVWILGKQHLLKTEKSKLLSDISARLWFTYRRKFSPIGGTGPSSDAGWGCMLRCGQMMLAQALICRHLGRDWSWEKQKEQPKEYQRILQCFLDRKDCCYSIHQMAQMGVGEGKSIGEWFGPNTVAQVLKKLALFDEWNSLAVYVSMDNTVVIEDIKKMCRVLPLSADTAGDRPPDSLTASNQSKGTSAYCSAWKPLLLIVPLRLGINQINPVYVDAFKECFKMPQSLGALGGKPNNAYYFIGFLGDELIFLDPHTTQTFVDTEENGTVNDQTFHCLQSPQRMNILNLDPSVALGFFCKEEKDFDNWCSLVQKEILKENLRMFELVQKHPS 357
               SCOP domains d2p82d_ D: Cysteine protease ATG4A                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------Peptidase_C54-2p82D01 D:39-338                                                                                                                                                                                                                                                                              ------------------- Pfam domains (1)
           Pfam domains (2) -------------Peptidase_C54-2p82D02 D:39-338                                                                                                                                                                                                                                                                              ------------------- Pfam domains (2)
           Pfam domains (3) -------------Peptidase_C54-2p82D03 D:39-338                                                                                                                                                                                                                                                                              ------------------- Pfam domains (3)
           Pfam domains (4) -------------Peptidase_C54-2p82D04 D:39-338                                                                                                                                                                                                                                                                              ------------------- Pfam domains (4)
         Sec.struct. author ..eeee..eeee...hhhhhhhhhhhh.....ee................hhhhhhhhhhhhhhhhhhhhh.....-.--..hhhhhhhhhh.........hhhhhhhhhhh.........hhhhhhhhhhhhhh.......eeee....eeehhhhhhhhh...----------------------------....eeeeeeee......hhhhhhhhhhhhhh..eeeeeeee..eeeeeeeee..eeeee.....ee...........hhhhh.....eeee.hhh..eeeeeeee.hhhhhhhhhhhhhhhh........eee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2        -----------------------Exon 1.5  PDB: D:65-98            ---------------------------------Exon 1.7  PDB: D:132-156 --------------------------Exon 1.9b  PDB: D:183-245 (gaps) UniProt: 183-245              Exon 1.10  PDB: D:246-272  ------------------------------------------------Exon 1.12a         Exon 1.13b         Transcript 1 (1)
           Transcript 1 (2) ---------------Exon 1.4  PDB: D:41-65   --------------------------------Exon 1.6  PDB: D:98-132 (gaps)     -----------------------Exon 1.8  PDB: D:156-183    ----------------------------------------------------------------------------------------Exon 1.11d  PDB: D:272-320 UniProt: 272-320      ------------------------------------- Transcript 1 (2)
                 2p82 D  26 DELVWILGKQHLLKTEKSKLLSDISARLWFTYRRKFSPIGGTGPSSDAGWGCMLRCGQMMLAQALICRHLGRDWSW-K--EQPKEYQRILQCFLDRKDCCYSIHQMAQMGVGEGKSIGEWFGPNTVAQVLKKLALFDEWNSLAVYVSMDNTVVIEDIKKMCRVLP----------------------------AWKPLLLIVPLRLGINQINPVYVDAFKECFKMPQSLGALGGKPNNAYYFIGFLGDELIFLDPHTTQTFVDTEENGTVNDQTFHCLQSPQRMNILNLDPSVALGFFCKEEKDFDNWCSLVQKEILKENLRMFELVQKHPS 357
                                    35        45        55        65        75        85        95     | | -|      115       125       135       145       155       165       175       185    |    -         -         -   |   225       235       245       255       265       275       285       295       305       315       325       335       345       355  
                                                                                                     101 |  |                                                                                 190                          219                                                                                                                                          
                                                                                                       103  |                                                                                                                                                                                                                                                           
                                                                                                          106

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Cysteine proteinases (392)

Superfamily: Cysteine proteinases (392)

Family: Autophagin-like (6)

Protein domain: Cysteine protease ATG4A (1)

Human (Homo sapiens) [TaxId: 9606] (1)

1a	d2p82a1	A:26-359
1b	d2p82b_	B:
1c	d2p82c_	C:
1d	d2p82d_	D:

(no "CATH Domain" information available for 2P82)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_CA (169)

Family: Peptidase_C54 (3)

Homo sapiens (Human) (3)

1a	Peptidase_C54-2p82D01	D:39-338
1b	Peptidase_C54-2p82D02	D:39-338
1c	Peptidase_C54-2p82D03	D:39-338
1d	Peptidase_C54-2p82D04	D:39-338

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (ATG4A_HUMAN | Q8WYN0)

molecular function
	GO:0004197	cysteine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	GO:0008234	cysteine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0006501	C-terminal protein lipidation	The covalent attachment of a lipid group to the carboxy terminus of a protein.
	GO:0000045	autophagosome assembly	The formation of a double membrane-bounded structure, the autophagosome, that occurs when a specialized membrane sac, called the isolation membrane, starts to enclose a portion of the cytoplasm.
	GO:0006914	autophagy	The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
	GO:0000422	autophagy of mitochondrion	The autophagic process in which mitochondria are delivered to the vacuole and degraded in response to changing cellular conditions.
	GO:0044804	autophagy of nucleus	A selective form of autophagy, by which damaged or non-essential parts of the nucleus, or even an entire nucleus is degraded.
	GO:0051697	protein delipidation	The breakage of covalent bonds to detach lipid groups from a protein.
	GO:0016485	protein processing	Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.
	GO:0006612	protein targeting to membrane	The process of directing proteins towards a membrane, usually using signals contained within the protein.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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	2p82
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(no "Related Entries Specified in the PDB File" available for 2P82)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 16)

Sites (16, 16)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (11, 44)

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SCOP Domains (1, 4)

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Pfam Domains (1, 4)

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