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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF THE D714A MUTANT OF RB69 DNA POLYMERASE
 
Authors :  K. E. Guja, A. Jacewicz, A. Trzemecka, D. Plochocka, E. Yakubovskaya, A M. Garcia-Diaz
Date :  30 Apr 13  (Deposition) - 09 Oct 13  (Release) - 23 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,E,F  (1x)
Keywords :  Palm Subdomain, Hydrolase, Transferase, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Jacewicz, A. Trzemecka, K. E. Guja, D. Plochocka, E. Yakubovskaya, A. Bebenek, M. Garcia-Diaz
A Remote Palm Domain Residue Of Rb69 Dna Polymerase Is Critical For Enzyme Activity And Influences The Conformatio Of The Active Site.
Plos One V. 8 76700 2013
PubMed-ID: 24116139  |  Reference-DOI: 10.1371/JOURNAL.PONE.0076700

(-) Compounds

Molecule 1 - DNA POLYMERASE
    Chains: A, B
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: 43
    Mutation: YES
    Organism Scientific: ENTEROBACTERIA PHAGE RB69
    Organism Taxid: 12353
    Synonym: GP43
 
Molecule 2 - DNA (5'- D(*TP*CP*AP*CP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
    Chains: C, E
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*C)-3')
    Chains: D, F
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A CD  
Biological Unit 2 (1x):  B  EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric Unit (5, 15)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2GOL2Ligand/IonGLYCEROL
3NA1Ligand/IonSODIUM ION
4SO46Ligand/IonSULFATE ION
5XG44Ligand/Ion2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL2Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
4SO45Ligand/IonSULFATE ION
5XG42Ligand/Ion2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL-1Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
4SO41Ligand/IonSULFATE ION
5XG42Ligand/Ion2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:36 , PHE A:38 , LYS A:48 , TYR A:49 , ARG A:59 , GLY A:84 , MET A:85 , ASP A:95 , PHE A:370 , LYS A:374 , LYS A:378 , VAL A:379 , ILE A:380BINDING SITE FOR RESIDUE XG4 A 1001
02AC2SOFTWAREASP A:623 , HOH A:1126 , HOH A:1317 , XG4 C:101BINDING SITE FOR RESIDUE CA A 1002
03AC3SOFTWARETHR A:413 , SER A:414 , ARG A:482 , LYS A:486 , LYS A:560 , HOH A:1126BINDING SITE FOR RESIDUE SO4 A 1003
04AC4SOFTWARETRP A:216 , ASN A:217 , SER A:289 , LEU A:290BINDING SITE FOR RESIDUE SO4 A 1004
05AC5SOFTWAREGLY A:637 , GLU A:638 , SER A:639BINDING SITE FOR RESIDUE SO4 A 1005
06AC6SOFTWARETYR A:49 , ARG A:59 , HOH A:1151BINDING SITE FOR RESIDUE SO4 A 1006
07AC7SOFTWAREHIS A:105 , VAL A:110BINDING SITE FOR RESIDUE SO4 A 1007
08AC8SOFTWAREILE A:557 , LEU A:561 , ASN A:564 , XG4 C:101BINDING SITE FOR RESIDUE GOL A 1008
09AC9SOFTWAREPHE A:650 , LYS A:653 , PHE A:654 , ARG A:658BINDING SITE FOR RESIDUE GOL A 1009
10BC1SOFTWARETYR A:619 , ASP A:621 , LYS A:706 , DA D:114 , DC D:115BINDING SITE FOR RESIDUE NA A 1010
11BC2SOFTWARELEU A:415 , TYR A:416 , LYS A:560 , ASN A:564 , THR A:622 , ASP A:623 , CA A:1002 , GOL A:1008 , HOH A:1114 , HOH A:1317 , DC C:4 , DG C:5 , HOH C:201 , DC D:115BINDING SITE FOR RESIDUE XG4 C 101
12BC3SOFTWARESER B:36 , PHE B:38 , TYR B:49 , GLY B:84 , MET B:85 , ASP B:95 , PHE B:370 , LYS B:374 , ASN B:377 , LYS B:378 , VAL B:379 , ILE B:380 , HOH B:1101BINDING SITE FOR RESIDUE XG4 B 1001
13BC4SOFTWARELEU B:415 , TYR B:416 , LYS B:560 , ASN B:564 , THR B:622 , ASP B:623 , SO4 B:1003 , CA B:1004 , DC E:4 , DG E:5 , DC F:115BINDING SITE FOR RESIDUE XG4 B 1002
14BC5SOFTWARETHR B:413 , SER B:414 , ARG B:482 , LYS B:560 , XG4 B:1002BINDING SITE FOR RESIDUE SO4 B 1003
15BC6SOFTWAREASP B:623 , XG4 B:1002BINDING SITE FOR RESIDUE CA B 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4KHN)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4KHN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KHN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KHN)

(-) Exons   (0, 0)

(no "Exon" information available for 4KHN)

(-) 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:901
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4khna1 A:1-375 Exonuclease domain of family B DNA polymerases                                                                                                                                                                                                                                                                                                                         d4khna2 A:376-901 Family B DNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee..eeeeeee.....eeeeee....eeeee.........ee.....eeeee..hhhhhhhhhhhhhhhh.......hhhhhhhhhhh......hhhhh.eeeeeee..................eeeeee....eeeeeee.ee..ee....hhhhhhhhhhhh....hhhhhh.eeeeee.hhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhhhhhhhh....eeeeeee....eeeeeee...ee.hhhhhhhhhh.......hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.ee......................ee...eeeeee.hhhhhhhhhhh.....eeee....hhhhhhh..........ee....eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee..eeeeehhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeee..........eeeee..eeeeeeeee..eeeeeeeeeee.hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee...hhh.ee..ee....hhhhhhhhhhhhhhh............eeeeee..........eeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4khn A   1 MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYFDIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYEIKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFDLLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAKRLSPHRKTRVKVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPIPNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWTGKKRYALNVWAMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPSGTEITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDMF 901
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900 


Chain B from PDB  Type:PROTEIN  Length:870
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4khnb1 B:1-375 Exonuclease domain of family B DNA polymerases                                                                                                                                                                                                                                                                                                                         d4khnb2 B:376-901 Family B DNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee..eeeeeee.....eeeeee....eeeee........eee....eeeeee..hhhhhhhhhhhhhhhh..ee...hhhhhhhhhhh......hhhhh.eeeeeeee...............eeeeeeee....eeeeeee...........hhhhhhhhhhhh....hhhhhh.eeeeee.hhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhh..hhhhhhhhh....eeeeeee....eeeeeee...ee.hhhhhhhhhh.......hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh..ee......................ee...eeeeee.hhhhhhhhhhh.....eeee....hhhhhhh..........ee....eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee..eeeeehhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeee..........eeeee..eeeeeeeee..eeeeeeeeeee.hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeee...hhh.ee..ee....hhhhhhhhhhhhhhh............eeeeee..........eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4khn B   1 MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYFDIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYEIKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFDLLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAKRLSPHRKTRVKVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPIPNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWTGKKRYALNVWAMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPSGTEITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDMF 901
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500  ||   541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                503|                                                                                                                                                                                                                                                                                                                                                                              
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 535                                                                                                                                                                                                                                                                                                                                                                              


Chain C from PDB  Type:DNA  Length:18
                                                  
                 4khn C   1 TCACGTAAGCAGTCCGCG  18
                                    10        


Chain D from PDB  Type:DNA  Length:13
                                             
                 4khn D 103 GCGGACTGCTTAC 115
                                   112   


Chain E from PDB  Type:DNA  Length:18
                                                  
                 4khn E   1 TCACGTAAGCAGTCCGCG  18
                                    10        


Chain F from PDB  Type:DNA  Length:13
                                             
                 4khn F 103 GCGGACTGCTTAC 115
                                   112
   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  (2, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KHN)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KHN)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)

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  4khn
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  DPOL_BPR69 | Q38087
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  2.7.7.7
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DPOL_BPR69 | Q38087: 1b1f 1b8h 1clq 1ig9 1ih7 1q9x 1q9y 1qe4 1waf 1wag 1wah 1wai 1waj 2atq 2dtu 2dy4 2oyq 2ozm 2ozs 2p5g 2p5o 3cfo 3cfp 3cfr 3cq8 3kd1 3kd5 3l8b 3lds 3lzi 3lzj 3nae 3nci 3ndk 3ne6 3ngi 3nhg 3qei 3qep 3qer 3qes 3qet 3qev 3qew 3qex 3qnn 3qno 3rma 3rmb 3rmc 3rmd 3rwu 3s9h 3scx 3si6 3sjj 3snn 3spy 3spz 3sq0 3sq1 3sq2 3sq4 3sun 3suo 3sup 3suq 3tab 3tae 3taf 3tag 3uiq 4dtj 4dtm 4dtn 4dto 4dtp 4dtr 4dts 4dtu 4dtx 4du1 4du3 4du4 4e3s 4fj5 4fj7 4fj8 4fj9 4fjg 4fjh 4fji 4fjj 4fjk 4fjl 4fjm 4fjn 4fjx 4fk0 4fk2 4fk4 4i9l 4i9q 4j2a 4j2b 4j2d 4j2e 4khq 4khs 4khu 4khw 4khy 4ki4 4ki6 4m3r 4m3t 4m3u 4m3w 4m3x 4m3y 4m3z 4m41 4m42 4m45

(-) Related Entries Specified in the PDB File

4i9l 4i9q