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