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Description

Title :   MONOCLINIC HEN EGG-WHITE LYSOZYME CRYSTALLIZED AT PH4.5 FORM HEAVY WATER SOLUTION

Authors :   K. Harata, T. Akiba

Date :   20 Oct 05 (Deposition) - 11 Jul 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.16

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

Keywords :   Phase Transition, Rigid-Body Motion, Tls Analysis, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Harata, T. Akiba
Structural Phase Transition Of Monoclinic Crystals Of Hen Egg-White Lysozyme
Acta Crystallogr. , Sect. D V. 62 375 2006
PubMed-ID: 16552138 | Reference-DOI: 10.1107/S0907444906001314

Compounds

Molecule 1 - LYSOZYME C
	Chains	:	A, B
	EC Number	:	3.2.1.17
	Organism Common	:	CHICKEN
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031
	Synonym	:	1,4-BETA-N-ACETYLMURAMIDASE C, ALLERGEN GAL D 4, GAL D IV

Structural Features

Chains, Units

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 240)

Asymmetric Unit (3, 240)

No.	Name	Count	Type	Full Name
1	DOD	234	Ligand/Ion
2	NA	1	Ligand/Ion	SODIUM ION
3	NO3	5	Ligand/Ion	NITRATE ION

Biological Unit 1 (2, 124)

No.	Name	Count	Type	Full Name
1	DOD	123	Ligand/Ion
2	NA	-1	Ligand/Ion	SODIUM ION
3	NO3	1	Ligand/Ion	NITRATE ION

Biological Unit 2 (2, 115)

No.	Name	Count	Type	Full Name
1	DOD	111	Ligand/Ion
2	NA	-1	Ligand/Ion	SODIUM ION
3	NO3	4	Ligand/Ion	NITRATE ION

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:65 , ASN A:74 , ASN A:77 , ILE A:78 , PRO A:79 , DOD A:545 , DOD A:596 , LYS B:316	BINDING SITE FOR RESIDUE NO3 A 401
2	AC2	SOFTWARE	ARG A:112 , LYS A:116 , ASN B:265 , ASN B:274 , ASN B:277 , ILE B:278 , PRO B:279	BINDING SITE FOR RESIDUE NO3 B 402
3	AC3	SOFTWARE	ARG A:21 , GLY A:22 , ASN B:265 , ASP B:266 , ARG B:268 , CYS B:280 , SER B:281	BINDING SITE FOR RESIDUE NO3 B 403
4	AC4	SOFTWARE	GLY B:326	BINDING SITE FOR RESIDUE NO3 B 404
5	AC5	SOFTWARE	SER B:260 , CYS B:264 , ASN B:265 , ASP B:266 , GLY B:267 , ARG B:268 , THR B:269 , SER B:272 , ARG B:273 , NA B:406	BINDING SITE FOR RESIDUE NO3 B 405
6	AC6	SOFTWARE	SER B:260 , CYS B:264 , SER B:272 , ARG B:273 , NO3 B:405 , DOD B:407 , DOD B:409	BINDING SITE FOR RESIDUE NA B 406

SS Bonds (8, 8)

Asymmetric Unit

No.	Residues
1	A:6	-	A:127
2	A:30	-	A:115
3	A:64	-	A:80
4	A:76	-	A:94
5	B:206	-	B:327
6	B:230	-	B:315
7	B:264	-	B:280
8	B:276	-	B:294

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 2D4I)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 2D4I)

PROSITE Motifs (2, 4)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LACTALBUMIN_LYSOZYME_2	PS51348	Alpha-lactalbumin / lysozyme C family profile.	LYSC_CHICK	19-147	2	A:1-129 B:201-329
2	LACTALBUMIN_LYSOZYME_1	PS00128	Alpha-lactalbumin / lysozyme C signature.	LYSC_CHICK	94-112	2	A:76-94 B:276-294

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LACTALBUMIN_LYSOZYME_2	PS51348	Alpha-lactalbumin / lysozyme C family profile.	LYSC_CHICK	19-147	1	A:1-129 -
2	LACTALBUMIN_LYSOZYME_1	PS00128	Alpha-lactalbumin / lysozyme C signature.	LYSC_CHICK	94-112	1	A:76-94 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LACTALBUMIN_LYSOZYME_2	PS51348	Alpha-lactalbumin / lysozyme C family profile.	LYSC_CHICK	19-147	1	- B:201-329
2	LACTALBUMIN_LYSOZYME_1	PS00128	Alpha-lactalbumin / lysozyme C signature.	LYSC_CHICK	94-112	1	- B:276-294

Exons (4, 8)

Asymmetric Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENSGALT00000016196	1a	ENSGALE00000107726	chr1:37298007-37298210	204	LYSC_CHICK	1-46	46	2	A:1-28 B:201-228	28 28
1.2	ENSGALT00000016196	2	ENSGALE00000107723	chr1:37299463-37299624	162	LYSC_CHICK	46-100	55	2	A:28-82 B:228-282	55 55
1.3	ENSGALT00000016196	3	ENSGALE00000107724	chr1:37301396-37301474	79	LYSC_CHICK	100-126	27	2	A:82-108 B:282-308	27 27
1.4a	ENSGALT00000016196	4a	ENSGALE00000107725	chr1:37301556-37301734	179	LYSC_CHICK	126-147	22	2	A:108-129 B:308-329	22 22

Sequences/Alignments

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:129
 aligned with LYSC_CHICK | P00698 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:129
                                    28        38        48        58        68        78        88        98       108       118       128       138         
           LYSC_CHICK    19 KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL 147
               SCOP domains d2d4ia_ A: Lysozyme                                                                                                               SCOP domains
               CATH domains 2d4iA00 A:1-129  [code=1.10.530.10, no name defined]                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....eee.....eee....ee...................hhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhh...hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) LACTALBUMIN_LYSOZYME_2  PDB: A:1-129 UniProt: 19-147                                                                              PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------LACTALBUMIN_LYSOZYM----------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1a  PDB: A:1-28      -----------------------------------------------------Exon 1.3  PDB: A:82-108    --------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------Exon 1.2  PDB: A:28-82 UniProt: 46-100                 -------------------------Exon 1.4a              Transcript 1 (2)
                 2d4i A   1 KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL 129
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:129
 aligned with LYSC_CHICK | P00698 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:129
                                    28        38        48        58        68        78        88        98       108       118       128       138         
           LYSC_CHICK    19 KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL 147
               SCOP domains d2d4ib_ B: Lysozyme                                                                                                               SCOP domains
               CATH domains 2d4iB00 B:201-329  [code=1.10.530.10, no name defined]                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....eee.....eee....ee...................hhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhh...hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) LACTALBUMIN_LYSOZYME_2  PDB: B:201-329 UniProt: 19-147                                                                            PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------LACTALBUMIN_LYSOZYM----------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1a  PDB: B:201-228   -----------------------------------------------------Exon 1.3  PDB: B:282-308   --------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------Exon 1.2  PDB: B:228-282 UniProt: 46-100               -------------------------Exon 1.4a              Transcript 1 (2)
                 2d4i B 201 KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL 329
                                   210       220       230       240       250       260       270       280       290       300       310       320

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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Lysozyme-like (1361)

Superfamily: Lysozyme-like (1361)

Family: C-type lysozyme (738)

Protein domain: Lysozyme (696)

Chicken (Gallus gallus) [TaxId: 9031] (459)

1a	d2d4ia_	A:
1b	d2d4ib_	B:

CATH Domains (1, 2)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Lysozyme (1131)

Homologous Superfamily: [code=1.10.530.10, no name defined] (605)

Chicken (Gallus gallus) (228)

1a	2d4iA00	A:1-129
1b	2d4iB00	B:201-329

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 2D4I)

Gene Ontology (13, 13)

Asymmetric Unit(hide GO term definitions)

Chain A,B (LYSC_CHICK | P00698)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	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:0016798	hydrolase activity, acting on glycosyl bonds	Catalysis of the hydrolysis of any glycosyl bond.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0003796	lysozyme activity	Catalysis of the hydrolysis of the beta-(1->4) linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan.
	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:0019835	cytolysis	The rupture of cell membranes and the loss of cytoplasm.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0001895	retina homeostasis	A tissue homeostatic process involved in the maintenance of an internal equilibrium within the retina of the eye, including control of cellular proliferation and death and control of metabolic function.
cellular component
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	LYSC_CHICK \| P00698	:	132l 193l 194l 1a2y 1aki 1at5 1at6 1azf 1b0d 1b2k 1bgi 1bhz 1bvk 1bvx 1bwh 1bwi 1bwj 1c08 1c10 1dpw 1dpx 1dqj 1e8l 1f0w 1f10 1f3j 1fdl 1flq 1flu 1flw 1fly 1fn5 1g7h 1g7i 1g7j 1g7l 1g7m 1gpq 1gwd 1gxv 1gxx 1h6m 1h87 1hc0 1hel 1hem 1hen 1heo 1hep 1heq 1her 1hew 1hf4 1hsw 1hsx 1ic4 1ic5 1ic7 1iee 1io5 1ioq 1ior 1ios 1iot 1ir7 1ir8 1ir9 1j1o 1j1p 1j1x 1ja2 1ja4 1ja6 1ja7 1jis 1jit 1jiy 1jj0 1jj1 1jj3 1jpo 1jto 1jtt 1kip 1kiq 1kir 1kxw 1kxx 1kxy 1lcn 1lj3 1lj4 1lje 1ljf 1ljg 1ljh 1lji 1ljj 1ljk 1lkr 1lks 1lma 1lpi 1lsa 1lsb 1lsc 1lsd 1lse 1lsf 1lsg 1lsm 1lsn 1lsy 1lsz 1lyo 1lys 1lyz 1lz8 1lz9 1lza 1lzb 1lzc 1lzd 1lze 1lzg 1lzh 1lzn 1lzt 1mel 1mlc 1n4f 1nby 1nbz 1ndg 1ndm 1p2c 1ps5 1qio 1qtk 1rcm 1rfp 1ri8 1rjc 1sf4 1sf6 1sf7 1sfb 1sfg 1sq2 1t3p 1t6v 1ua6 1uc0 1uco 1uia 1uib 1uic 1uid 1uie 1uif 1uig 1uih 1uuz 1v7s 1v7t 1vat 1vau 1vdp 1vdq 1vds 1vdt 1ved 1vfb 1w6z 1wtm 1wtn 1xei 1xej 1xek 1xfp 1xgp 1xgq 1xgr 1xgt 1xgu 1yik 1yil 1ykx 1yky 1ykz 1yl0 1yl1 1yqv 1z55 1zmy 1zv5 1zvh 1zvy 2a6u 2a7d 2a7f 2aub 2b5z 2blx 2bly 2bpu 2c8o 2c8p 2cds 2cgi 2d4j 2d4k 2d6b 2d91 2dqc 2dqd 2dqe 2dqf 2dqg 2dqh 2dqi 2dqj 2eiz 2eks 2epe 2f2n 2f30 2f4a 2f4g 2fbb 2g4p 2g4q 2h9j 2h9k 2hfm 2hs7 2hs9 2hso 2htx 2hu1 2hu3 2hub 2i25 2i26 2i6z 2iff 2lym 2lyo 2lyz 2lzh 2lzt 2pc2 2q0m 2vb1 2w1l 2w1m 2w1x 2w1y 2war 2x0a 2xbr 2xbs 2xjw 2xth 2ybh 2ybi 2ybj 2ybl 2ybm 2ybn 2ydg 2yss 2yvb 2z12 2z18 2z19 2znw 2znx 2zq3 2zq4 2zyp 3a34 3a3q 3a3r 3a67 3a6b 3a6c 3a8z 3a90 3a91 3a92 3a93 3a94 3a95 3a96 3agg 3agh 3agi 3ajn 3atn 3ato 3aw6 3aw7 3az4 3az5 3az6 3az7 3b6l 3b72 3d9a 3e3d 3ems 3exd 3f6z 3g3a 3g3b 3hfm 3iju 3ijv 3j4g 3j6k 3kam 3lym 3lyo 3lyt 3lyz 3lzt 3m18 3m3u 3mbe 3n9a 3n9c 3n9e 3ojp 3ok0 3otp 3p4z 3p64 3p65 3p66 3p68 3qe8 3qng 3qy4 3rnx 3rt5 3ru5 3rw8 3rz4 3sp3 3t6u 3tmu 3tmv 3tmw 3tmx 3txb 3txd 3txe 3txf 3txg 3txh 3txi 3txj 3txk 3ulr 3w6a 3wl2 3wmk 3wpj 3wpk 3wpl 3wu7 3wu8 3wu9 3wua 3wul 3wum 3wun 3wvx 3wvy 3ww5 3ww6 3wxt 3wxu 3zek 3zvq 4a7d 4a8a 4a8b 4aga 4axt 4b0d 4b1a 4b49 4b4e 4b4i 4b4j 4bad 4baf 4bap 4bs7 4c3w 4cj2 4d9z 4dc4 4dd0 4dd1 4dd2 4dd3 4dd7 4dd9 4dda 4ddb 4ddc 4dt3 4e3u 4eof 4et8 4et9 4eta 4etb 4etc 4etd 4ete 4fjr 4g49 4g4b 4g4c 4g4h 4gcb 4gcc 4gcd 4gce 4gcf 4gla 4glv 4gn3 4gn4 4gn5 4h1p 4h8x 4h8y 4h8z 4h90 4h91 4h92 4h93 4h94 4h9a 4h9b 4h9c 4h9e 4h9f 4h9h 4h9i 4hp0 4hpi 4hsf 4htk 4htn 4htq 4hv1 4hv2 4i8s 4ias 4iat 4ii8 4j1a 4j1b 4j7v 4kxi 4lfp 4lfx 4lgk 4lt0 4lt1 4lt2 4lt3 4lyb 4lyc 4lym 4lyo 4lyt 4lyz 4lzt 4m4o 4m6d 4mr1 4n0j 4n1c 4n1e 4n5r 4n8z 4n9r 4neb 4nfv 4ng1 4ng8 4ngi 4ngj 4ngk 4ngl 4ngo 4ngv 4ngw 4ngy 4ngz 4nhi 4nhp 4nhq 4nhs 4nht 4nij 4nsg 4nsh 4nsi 4nsj 4nwe 4nwh 4ny5 4o34 4ooo 4oot 4owa 4owb 4owc 4owe 4owh 4p2e 4pgj 4phi 4ppo 4prq 4pru 4qeq 4qgz 4qy9 4r0f 4r6c 4rds 4rlm 4rln 4rw1 4rw2 4tsa 4tsb 4tsc 4ttd 4tun 4tws 4u3x 4uwn 4uwu 4uwv 4w94 4w96 4wg1 4wg7 4wl6 4wl7 4wld 4wlt 4wlx 4wly 4wm1 4wm2 4wm3 4wm4 4wm5 4wm6 4wmg 4wo6 4wo9 4woa 4x3b 4xad 4xen 4xjb 4xjd 4xjf 4xjg 4xjh 4xji 4xn6 4xyy 4yem 4yen 4yeo 4ym8 4yop 4z3m 4z41 4z46 4z98 4zee 4zfp 4zix 5a3e 5a3z 5amy 5apc 5apd 5ape 5apf 5b05 5b06 5b07 5b1f 5b1g 5b59 5b5j 5c6i 5c6j 5c6l 5d5c 5d5f 5dl9 5dla 5dm9 5e4p 5e9r 5ebh 5f14 5f16 5f81 5f9u 5f9x 5fcp 5fdj 5fek 5fel 5fhw 5fst 5hll 5hmj 5hmv 5hnc 5hnl 5hq1 5i4w 5i4x 5i4y 5i53 5i54 5i5q 5idd 5iel 5ihg 5ii3 5ilc 5ilf 5j7c 5jen 5k2k 5k2n 5k2p 5k2q 5k2r 5k2s 5k7o 5kj9 5kki 5kkj 5kxk 5kxl 5kxm 5kxn 5kxo 5kxp 5kxr 5kxs 5kxt 5kxw 5kxx 5kxy 5kxz 5ky1 5l3h 5l3i 5l9j 5la5 5la8 5laf 5lag 5lin 5lio 5lvg 5lvh 5lvi 5lvj 5lxw 5lym 5lyt 5lyz 5m1y 5myy 5nbj 5ne0 5t3f 5tk0 5uvj 5v4g 5v4h 5v4i 6lyt 6lyz 7lyz 8lyz 9lyz

Related Entries Specified in the PDB File

2d4j	MONOCLINIC HEN EGG-WHITE LYSOZYME CRYSTALLIZED FROM A HEAVY WATER SOLUTION AT PD 4.5
2d4k	MONOCLINIC HEN EGG-WHITE LYSOZYME CRYSTALLIZED AT PH 7.6, 313K