This benchmark case is special. Because the alignments below align only the residues visible in the
electron densities, you cannot see that there are many residues missing in BOTH bound and unbound
structures. More importantly, there is a loop missing in the unbound structure 1E8Z_A that the authors
show is important in binding. To dock this complex, we strongly recommend rebuilding at least the
255-267 loop.

NOTE THAT IN THE ALIGNMENTS BELOW, GAPS MOST LIKELY INDICATE
RESIDUES MISSING IN THE ELECTRON DENSITY.

Alignment: 1HE8_A against 1E8Z_A
Query= 
         (749 letters)

>1E8Z_A
          Length = 839

 Score =  842 bits (2176), Expect = 0.0
 Identities = 430/451 (95%), Positives = 430/451 (95%), Gaps = 21/451 (4%)

Query: 320 SALDVGLTMQLLDCNFSDENVRAIAVQKLESLEDDDVLHYLLQLVQAVKFEPYHDSALAR 379
           SALDVGLTMQLLDCNFSDENVRAIAVQKLESLEDDDVLHYLLQLVQAVKFEPYHDSALAR
Sbjct: 381 SALDVGLTMQLLDCNFSDENVRAIAVQKLESLEDDDVLHYLLQLVQAVKFEPYHDSALAR 440

Query: 380 FLLKRGLRNKRIGHFLFWFLRSEIAQSRHYQQRFAVILEAYLRGCGTAMLHDFTQQVQVI 439
           FLLKRGLRNKRIGHFLFWFLRSEIAQSRHYQQRFAVILEAYLRGCGTAMLHDFTQQVQVI
Sbjct: 441 FLLKRGLRNKRIGHFLFWFLRSEIAQSRHYQQRFAVILEAYLRGCGTAMLHDFTQQVQVI 500

Query: 440 EMLQKVTLDIKSLS-------SQVISQLKQKLENLQNSQLPESFRVPYDPGLKAGALAIE 492
           EMLQKVTLDIKSLS       SQVISQLKQKLENLQNSQLPESFRVPYDPGLKAGALAIE
Sbjct: 501 EMLQKVTLDIKSLSAEKYDVSSQVISQLKQKLENLQNSQLPESFRVPYDPGLKAGALAIE 560

Query: 493 KCKVMASKKKPLWLEFKCADPTALSNETIGIIFKHGDDLRQDMLILQILRIMESIWETES 552
           KCKVMASKKKPLWLEFKCADPTALSNETIGIIFKHGDDLRQDMLILQILRIMESIWETES
Sbjct: 561 KCKVMASKKKPLWLEFKCADPTALSNETIGIIFKHGDDLRQDMLILQILRIMESIWETES 620

Query: 553 LDLCLLPYGCISTGDKIGMIEIVKDATTIAKIQQST-----FKDEVLNHWLKEKSPTEEK 607
           LDLCLLPYGCISTGDKIGMIEIVKDATTIAKIQQST     FKDEVLNHWLKEKSPTEEK
Sbjct: 621 LDLCLLPYGCISTGDKIGMIEIVKDATTIAKIQQSTVGNTGFKDEVLNHWLKEKSPTEEK 680

Query: 608 FQAAVERFVYSCAGYCVATFVLGIGDRHNDNIMITETGNLFHIDFGHERVPFVLTPDFLF 667
           FQAAVERFVYSCAGYCVATFVLGIGDRHNDNIMITETGNLFHIDFGHERVPFVLTPDFLF
Sbjct: 681 FQAAVERFVYSCAGYCVATFVLGIGDRHNDNIMITETGNLFHIDFGHERVPFVLTPDFLF 740

Query: 668 VMGTSGKKTSPHFQKFQDICVKAYLALRHHTNLLIILFSMMLMT---------DIEYIRD 718
           VMGTSGKKTSPHFQKFQDICVKAYLALRHHTNLLIILFSMMLMT         DIEYIRD
Sbjct: 741 VMGTSGKKTSPHFQKFQDICVKAYLALRHHTNLLIILFSMMLMTGMPQLTSKEDIEYIRD 800

Query: 719 ALTVGKNEEDAKKYFLDQIEVCRDKGWTVQF 749
           ALTVGKNEEDAKKYFLDQIEVCRDKGWTVQF
Sbjct: 801 ALTVGKNEEDAKKYFLDQIEVCRDKGWTVQF 831



 Score =  570 bits (1470), Expect = e-167
 Identities = 295/330 (89%), Positives = 299/330 (90%), Gaps = 28/330 (8%)

Query: 1   SEESQAFQRQLTALIGYDVTDVSNVHDDELEFTRRGLVTPRMAEVASRDPKLYAMHPWVT 60
           SEESQAFQRQLTALIGYDVTDVSNVHDDELEFTRRGLVTPRMAEVASRDPKLYAMHPWVT
Sbjct: 1   SEESQAFQRQLTALIGYDVTDVSNVHDDELEFTRRGLVTPRMAEVASRDPKLYAMHPWVT 60

Query: 61  SKPLPEYLWKKIANNCIFIKIHRSTTSQTIKVSPDDTPGAILQSFFTKMAKKKSLMDIPE 120
           SKPLPEYLWKKIANNCIFI IHRSTTSQTIKVSPDDTPGAILQSFFTKMAK         
Sbjct: 61  SKPLPEYLWKKIANNCIFIVIHRSTTSQTIKVSPDDTPGAILQSFFTKMAK--------- 111

Query: 121 SQSEQDFVLRVCGRDEYLVGETPIKNFQWVRHCLKNGEEIHVVLDTPPDPALDEVRKESL 180
                DFVLRVCGRDEYLVGETPIKNFQWVRHCLKNGEEIHVVLDTPPDPALDEVRKE  
Sbjct: 112 -----DFVLRVCGRDEYLVGETPIKNFQWVRHCLKNGEEIHVVLDTPPDPALDEVRKE-- 164

Query: 181 WDCDRKFRVKIRGIDIPVLP----LTVFVEANIQHGQQVLCQRRTSPKPFTEEVLWNVWL 236
            +CDRKFRVKIRGIDIPVLP    LTVFVEANIQHGQQVLCQRRTSPKPFTEEVLWNVWL
Sbjct: 165 -ECDRKFRVKIRGIDIPVLPRNTDLTVFVEANIQHGQQVLCQRRTSPKPFTEEVLWNVWL 223

Query: 237 EFSIKIKDLPKGALLNLQIYCKVRLLYYVNLLLIDHRFLLRRGEYVLHMWQIS--NADKL 294
           EFSIKIKDLPKGALLNLQIYC   LLYYVNLLLIDHRFLLRRGEYVLHMWQIS  NADKL
Sbjct: 224 EFSIKIKDLPKGALLNLQIYC---LLYYVNLLLIDHRFLLRRGEYVLHMWQISGFNADKL 280

Query: 295 TSATNPDKENSMSISILLDNYCHPISALDV 324
           TSATNPDKENSMSISILLDN  HPI+  ++
Sbjct: 281 TSATNPDKENSMSISILLDN--HPIARAEM 308



 Score = 17.3 bits (33), Expect = 3.4
 Identities = 7/24 (29%), Positives = 12/24 (49%)

Query: 158 EEIHVVLDTPPDPALDEVRKESLW 181
           +++  ++ T P   L    KE LW
Sbjct: 314 KQLEAIIATDPLNPLTAEDKELLW 337



 Score = 16.9 bits (32), Expect = 4.5
 Identities = 6/7 (85%), Positives = 7/7 (99%)

Query: 273 RFLLRRG 279
           RFLL+RG
Sbjct: 440 RFLLKRG 446



 Score = 16.9 bits (32), Expect = 4.5
 Identities = 6/7 (85%), Positives = 7/7 (99%)

Query: 379 RFLLKRG 385
           RFLL+RG
Sbjct: 257 RFLLRRG 263


Alignment: 1HE8_B against 821P_
Query= 
         (166 letters)

>821P_
          Length = 166

 Score =  330 bits (845), Expect = 9e-96
 Identities = 165/166 (99%), Positives = 165/166 (99%)

Query: 1   MTEYKLVVVGAVGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG 60
           MTEYKLVVVGA GVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG
Sbjct: 1   MTEYKLVVVGAPGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG 60

Query: 61  QEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDL 120
           QEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDL
Sbjct: 61  QEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDL 120

Query: 121 AARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH 166
           AARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH
Sbjct: 121 AARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH 166