0.011364
0.000000
0.000000
0.000000
0.013175
0.000000
0.000000
0.000000
0.019802
0.00000
0.00000
0.00000
THE SIDE CHAINS OF ARG 44, LYS 59, AND LEU 61 HAVE POOR ELECTRON DENSITY, AND THE ATOMIC MODEL INCLUDES ONLY THE CB ATOMS FOR THESE SIDE CHAINS.
Louie, G.V.
Brownlie, P.D.
Lambert, R.
Cooper, J.B.
Blundell, T.L.
Wood, S.P.
Warren, M.J.
Woodcock, S.C.
Jordan, P.M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
88.000
75.900
50.500
C2 H4 O2
60.052
ACETIC ACID
non-polymer
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C20 H24 N2 O8
420.413
3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid
DIPYRROMETHANE COFACTOR
non-polymer
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
UK
Nature
NATUAS
0006
0028-0836
359
33
39
10.1038/359033a0
1522882
Structure of porphobilinogen deaminase reveals a flexible multidomain polymerase with a single catalytic site.
1992
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
x-ray
1
1.0
33891.805
PORPHOBILINOGEN DEAMINASE
2.5.1.61
1
man
polymer
420.413
3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid
1
syn
non-polymer
60.052
ACETIC ACID
1
syn
non-polymer
18.015
water
249
nat
water
no
no
MLDNVLRIATRQSPLALWQAHYVKDKLMASHPGLVVELVPMVTRGDVILDTPLAKVGGKGLFVKELEVALLENRADIAVH
SMKDVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDALPAGSIVGTSSLRRQCQLAERRPDLIIRSLRGNVGTRLSKLD
NGEYDAIILAVAGLKRLGLESRIRAALPPEISLPAVGQGAVGIECRLDDSRTRELLAALNHHETALRVTAERAMNTRLEG
ACQVPIGSYAELIDGEIWLRGLVGAPDGSQIIRGERRGAPQDAEQMGISLAEELLNNGAREILAEVYNGDAPA
MLDNVLRIATRQSPLALWQAHYVKDKLMASHPGLVVELVPMVTRGDVILDTPLAKVGGKGLFVKELEVALLENRADIAVH
SMKDVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDALPAGSIVGTSSLRRQCQLAERRPDLIIRSLRGNVGTRLSKLD
NGEYDAIILAVAGLKRLGLESRIRAALPPEISLPAVGQGAVGIECRLDDSRTRELLAALNHHETALRVTAERAMNTRLEG
ACQVPIGSYAELIDGEIWLRGLVGAPDGSQIIRGERRGAPQDAEQMGISLAEELLNNGAREILAEVYNGDAPA
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Escherichia
sample
562
Escherichia coli
2.49
50.54
pdbx_database_status
struct_conf
struct_conf_type
software
struct_conn
software
repository
Initial release
Version format compliance
Version format compliance
Non-polymer description
Derived calculations
Other
Data collection
Derived calculations
Refinement description
Data collection
Refinement description
1
0
1993-10-31
1
1
2008-03-03
1
2
2011-07-13
1
3
2013-09-18
1
4
2017-11-29
1
5
2019-07-17
1
6
2019-08-14
_pdbx_database_status.process_site
_software.classification
_struct_conn.pdbx_leaving_atom_flag
_software.classification
Y
BNL
1992-11-17
REL
REL
DPM
3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid
ACY
ACETIC ACID
HOH
water
DPM
314
2
DPM
DPM
314
A
ACY
315
3
ACY
ACY
315
A
HOH
401
4
HOH
HOH
401
A
HOH
402
4
HOH
HOH
402
A
HOH
403
4
HOH
HOH
403
A
HOH
404
4
HOH
HOH
404
A
HOH
405
4
HOH
HOH
405
A
HOH
406
4
HOH
HOH
406
A
HOH
407
4
HOH
HOH
407
A
HOH
408
4
HOH
HOH
408
A
HOH
409
4
HOH
HOH
409
A
HOH
410
4
HOH
HOH
410
A
HOH
411
4
HOH
HOH
411
A
HOH
412
4
HOH
HOH
412
A
HOH
413
4
HOH
HOH
413
A
HOH
414
4
HOH
HOH
414
A
HOH
415
4
HOH
HOH
415
A
HOH
416
4
HOH
HOH
416
A
HOH
417
4
HOH
HOH
417
A
HOH
418
4
HOH
HOH
418
A
HOH
419
4
HOH
HOH
419
A
HOH
420
4
HOH
HOH
420
A
HOH
421
4
HOH
HOH
421
A
HOH
422
4
HOH
HOH
422
A
HOH
423
4
HOH
HOH
423
A
HOH
424
4
HOH
HOH
424
A
HOH
425
4
HOH
HOH
425
A
HOH
426
4
HOH
HOH
426
A
HOH
427
4
HOH
HOH
427
A
HOH
428
4
HOH
HOH
428
A
HOH
429
4
HOH
HOH
429
A
HOH
430
4
HOH
HOH
430
A
HOH
431
4
HOH
HOH
431
A
HOH
432
4
HOH
HOH
432
A
HOH
433
4
HOH
HOH
433
A
HOH
434
4
HOH
HOH
434
A
HOH
435
4
HOH
HOH
435
A
HOH
436
4
HOH
HOH
436
A
HOH
437
4
HOH
HOH
437
A
HOH
438
4
HOH
HOH
438
A
HOH
439
4
HOH
HOH
439
A
HOH
440
4
HOH
HOH
440
A
HOH
441
4
HOH
HOH
441
A
HOH
442
4
HOH
HOH
442
A
HOH
443
4
HOH
HOH
443
A
HOH
444
4
HOH
HOH
444
A
HOH
445
4
HOH
HOH
445
A
HOH
446
4
HOH
HOH
446
A
HOH
447
4
HOH
HOH
447
A
HOH
448
4
HOH
HOH
448
A
HOH
449
4
HOH
HOH
449
A
HOH
450
4
HOH
HOH
450
A
HOH
451
4
HOH
HOH
451
A
HOH
452
4
HOH
HOH
452
A
HOH
453
4
HOH
HOH
453
A
HOH
454
4
HOH
HOH
454
A
HOH
455
4
HOH
HOH
455
A
HOH
456
4
HOH
HOH
456
A
HOH
457
4
HOH
HOH
457
A
HOH
458
4
HOH
HOH
458
A
HOH
459
4
HOH
HOH
459
A
HOH
460
4
HOH
HOH
460
A
HOH
461
4
HOH
HOH
461
A
HOH
462
4
HOH
HOH
462
A
HOH
463
4
HOH
HOH
463
A
HOH
464
4
HOH
HOH
464
A
HOH
465
4
HOH
HOH
465
A
HOH
466
4
HOH
HOH
466
A
HOH
467
4
HOH
HOH
467
A
HOH
468
4
HOH
HOH
468
A
HOH
469
4
HOH
HOH
469
A
HOH
470
4
HOH
HOH
470
A
HOH
471
4
HOH
HOH
471
A
HOH
472
4
HOH
HOH
472
A
HOH
473
4
HOH
HOH
473
A
HOH
474
4
HOH
HOH
474
A
HOH
475
4
HOH
HOH
475
A
HOH
476
4
HOH
HOH
476
A
HOH
477
4
HOH
HOH
477
A
HOH
478
4
HOH
HOH
478
A
HOH
479
4
HOH
HOH
479
A
HOH
480
4
HOH
HOH
480
A
HOH
481
4
HOH
HOH
481
A
HOH
482
4
HOH
HOH
482
A
HOH
484
4
HOH
HOH
484
A
HOH
485
4
HOH
HOH
485
A
HOH
486
4
HOH
HOH
486
A
HOH
487
4
HOH
HOH
487
A
HOH
488
4
HOH
HOH
488
A
HOH
489
4
HOH
HOH
489
A
HOH
490
4
HOH
HOH
490
A
HOH
492
4
HOH
HOH
492
A
HOH
493
4
HOH
HOH
493
A
HOH
494
4
HOH
HOH
494
A
HOH
495
4
HOH
HOH
495
A
HOH
496
4
HOH
HOH
496
A
HOH
497
4
HOH
HOH
497
A
HOH
498
4
HOH
HOH
498
A
HOH
499
4
HOH
HOH
499
A
HOH
500
4
HOH
HOH
500
A
HOH
501
4
HOH
HOH
501
A
HOH
502
4
HOH
HOH
502
A
HOH
503
4
HOH
HOH
503
A
HOH
504
4
HOH
HOH
504
A
HOH
505
4
HOH
HOH
505
A
HOH
506
4
HOH
HOH
506
A
HOH
507
4
HOH
HOH
507
A
HOH
508
4
HOH
HOH
508
A
HOH
509
4
HOH
HOH
509
A
HOH
510
4
HOH
HOH
510
A
HOH
511
4
HOH
HOH
511
A
HOH
512
4
HOH
HOH
512
A
HOH
513
4
HOH
HOH
513
A
HOH
514
4
HOH
HOH
514
A
HOH
515
4
HOH
HOH
515
A
HOH
516
4
HOH
HOH
516
A
HOH
517
4
HOH
HOH
517
A
HOH
518
4
HOH
HOH
518
A
HOH
519
4
HOH
HOH
519
A
HOH
520
4
HOH
HOH
520
A
HOH
521
4
HOH
HOH
521
A
HOH
522
4
HOH
HOH
522
A
HOH
523
4
HOH
HOH
523
A
HOH
524
4
HOH
HOH
524
A
HOH
525
4
HOH
HOH
525
A
HOH
526
4
HOH
HOH
526
A
HOH
527
4
HOH
HOH
527
A
HOH
528
4
HOH
HOH
528
A
HOH
529
4
HOH
HOH
529
A
HOH
530
4
HOH
HOH
530
A
HOH
531
4
HOH
HOH
531
A
HOH
532
4
HOH
HOH
532
A
HOH
533
4
HOH
HOH
533
A
HOH
534
4
HOH
HOH
534
A
HOH
535
4
HOH
HOH
535
A
HOH
536
4
HOH
HOH
536
A
HOH
537
4
HOH
HOH
537
A
HOH
538
4
HOH
HOH
538
A
HOH
539
4
HOH
HOH
539
A
HOH
540
4
HOH
HOH
540
A
HOH
541
4
HOH
HOH
541
A
HOH
542
4
HOH
HOH
542
A
HOH
543
4
HOH
HOH
543
A
HOH
544
4
HOH
HOH
544
A
HOH
545
4
HOH
HOH
545
A
HOH
546
4
HOH
HOH
546
A
HOH
548
4
HOH
HOH
548
A
HOH
549
4
HOH
HOH
549
A
HOH
550
4
HOH
HOH
550
A
HOH
551
4
HOH
HOH
551
A
HOH
552
4
HOH
HOH
552
A
HOH
553
4
HOH
HOH
553
A
HOH
554
4
HOH
HOH
554
A
HOH
555
4
HOH
HOH
555
A
HOH
556
4
HOH
HOH
556
A
HOH
557
4
HOH
HOH
557
A
HOH
558
4
HOH
HOH
558
A
HOH
559
4
HOH
HOH
559
A
HOH
560
4
HOH
HOH
560
A
HOH
561
4
HOH
HOH
561
A
HOH
562
4
HOH
HOH
562
A
HOH
563
4
HOH
HOH
563
A
HOH
564
4
HOH
HOH
564
A
HOH
565
4
HOH
HOH
565
A
HOH
566
4
HOH
HOH
566
A
HOH
567
4
HOH
HOH
567
A
HOH
568
4
HOH
HOH
568
A
HOH
569
4
HOH
HOH
569
A
HOH
570
4
HOH
HOH
570
A
HOH
571
4
HOH
HOH
571
A
HOH
572
4
HOH
HOH
572
A
HOH
573
4
HOH
HOH
573
A
HOH
574
4
HOH
HOH
574
A
HOH
575
4
HOH
HOH
575
A
HOH
576
4
HOH
HOH
576
A
HOH
577
4
HOH
HOH
577
A
HOH
578
4
HOH
HOH
578
A
HOH
579
4
HOH
HOH
579
A
HOH
580
4
HOH
HOH
580
A
HOH
581
4
HOH
HOH
581
A
HOH
582
4
HOH
HOH
582
A
HOH
583
4
HOH
HOH
583
A
HOH
584
4
HOH
HOH
584
A
HOH
585
4
HOH
HOH
585
A
HOH
586
4
HOH
HOH
586
A
HOH
587
4
HOH
HOH
587
A
HOH
588
4
HOH
HOH
588
A
HOH
589
4
HOH
HOH
589
A
HOH
590
4
HOH
HOH
590
A
HOH
591
4
HOH
HOH
591
A
HOH
592
4
HOH
HOH
592
A
HOH
593
4
HOH
HOH
593
A
HOH
594
4
HOH
HOH
594
A
HOH
595
4
HOH
HOH
595
A
HOH
596
4
HOH
HOH
596
A
HOH
597
4
HOH
HOH
597
A
HOH
598
4
HOH
HOH
598
A
HOH
599
4
HOH
HOH
599
A
HOH
600
4
HOH
HOH
600
A
HOH
601
4
HOH
HOH
601
A
HOH
602
4
HOH
HOH
602
A
HOH
603
4
HOH
HOH
603
A
HOH
604
4
HOH
HOH
604
A
HOH
605
4
HOH
HOH
605
A
HOH
606
4
HOH
HOH
606
A
HOH
607
4
HOH
HOH
607
A
HOH
608
4
HOH
HOH
608
A
HOH
609
4
HOH
HOH
609
A
HOH
610
4
HOH
HOH
610
A
HOH
611
4
HOH
HOH
611
A
HOH
612
4
HOH
HOH
612
A
HOH
613
4
HOH
HOH
613
A
HOH
614
4
HOH
HOH
614
A
HOH
615
4
HOH
HOH
615
A
HOH
616
4
HOH
HOH
616
A
HOH
617
4
HOH
HOH
617
A
HOH
618
4
HOH
HOH
618
A
HOH
619
4
HOH
HOH
619
A
HOH
620
4
HOH
HOH
620
A
HOH
621
4
HOH
HOH
621
A
HOH
622
4
HOH
HOH
622
A
HOH
623
4
HOH
HOH
623
A
HOH
624
4
HOH
HOH
624
A
HOH
625
4
HOH
HOH
625
A
HOH
626
4
HOH
HOH
626
A
HOH
627
4
HOH
HOH
627
A
HOH
628
4
HOH
HOH
628
A
HOH
629
4
HOH
HOH
629
A
HOH
630
4
HOH
HOH
630
A
HOH
631
4
HOH
HOH
631
A
HOH
632
4
HOH
HOH
632
A
HOH
633
4
HOH
HOH
633
A
HOH
634
4
HOH
HOH
634
A
HOH
635
4
HOH
HOH
635
A
HOH
636
4
HOH
HOH
636
A
HOH
637
4
HOH
HOH
637
A
HOH
638
4
HOH
HOH
638
A
HOH
639
4
HOH
HOH
639
A
HOH
640
4
HOH
HOH
640
A
HOH
641
4
HOH
HOH
641
A
HOH
642
4
HOH
HOH
642
A
HOH
643
4
HOH
HOH
643
A
HOH
644
4
HOH
HOH
644
A
HOH
645
4
HOH
HOH
645
A
HOH
646
4
HOH
HOH
646
A
HOH
647
4
HOH
HOH
647
A
HOH
648
4
HOH
HOH
648
A
HOH
649
4
HOH
HOH
649
A
HOH
650
4
HOH
HOH
650
A
HOH
651
4
HOH
HOH
651
A
HOH
652
4
HOH
HOH
652
A
n
1
1
A
n
2
2
A
ASP
3
n
3
ASP
3
A
ASN
4
n
4
ASN
4
A
VAL
5
n
5
VAL
5
A
LEU
6
n
6
LEU
6
A
ARG
7
n
7
ARG
7
A
ILE
8
n
8
ILE
8
A
ALA
9
n
9
ALA
9
A
THR
10
n
10
THR
10
A
ARG
11
n
11
ARG
11
A
GLN
12
n
12
GLN
12
A
SER
13
n
13
SER
13
A
PRO
14
n
14
PRO
14
A
LEU
15
n
15
LEU
15
A
ALA
16
n
16
ALA
16
A
LEU
17
n
17
LEU
17
A
TRP
18
n
18
TRP
18
A
GLN
19
n
19
GLN
19
A
ALA
20
n
20
ALA
20
A
HIS
21
n
21
HIS
21
A
TYR
22
n
22
TYR
22
A
VAL
23
n
23
VAL
23
A
LYS
24
n
24
LYS
24
A
ASP
25
n
25
ASP
25
A
LYS
26
n
26
LYS
26
A
LEU
27
n
27
LEU
27
A
MET
28
n
28
MET
28
A
ALA
29
n
29
ALA
29
A
SER
30
n
30
SER
30
A
HIS
31
n
31
HIS
31
A
PRO
32
n
32
PRO
32
A
GLY
33
n
33
GLY
33
A
LEU
34
n
34
LEU
34
A
VAL
35
n
35
VAL
35
A
VAL
36
n
36
VAL
36
A
GLU
37
n
37
GLU
37
A
LEU
38
n
38
LEU
38
A
VAL
39
n
39
VAL
39
A
PRO
40
n
40
PRO
40
A
MET
41
n
41
MET
41
A
VAL
42
n
42
VAL
42
A
THR
43
n
43
THR
43
A
ARG
44
n
44
ARG
44
A
GLY
45
n
45
GLY
45
A
ASP
46
n
46
ASP
46
A
VAL
47
n
47
VAL
47
A
ILE
48
n
48
ILE
48
A
n
49
49
A
n
50
50
A
n
51
51
A
n
52
52
A
n
53
53
A
n
54
54
A
n
55
55
A
n
56
56
A
n
57
57
A
GLY
58
n
58
GLY
58
A
LYS
59
n
59
LYS
59
A
GLY
60
n
60
GLY
60
A
LEU
61
n
61
LEU
61
A
PHE
62
n
62
PHE
62
A
VAL
63
n
63
VAL
63
A
LYS
64
n
64
LYS
64
A
GLU
65
n
65
GLU
65
A
LEU
66
n
66
LEU
66
A
GLU
67
n
67
GLU
67
A
VAL
68
n
68
VAL
68
A
ALA
69
n
69
ALA
69
A
LEU
70
n
70
LEU
70
A
LEU
71
n
71
LEU
71
A
GLU
72
n
72
GLU
72
A
ASN
73
n
73
ASN
73
A
ARG
74
n
74
ARG
74
A
ALA
75
n
75
ALA
75
A
ASP
76
n
76
ASP
76
A
ILE
77
n
77
ILE
77
A
ALA
78
n
78
ALA
78
A
VAL
79
n
79
VAL
79
A
HIS
80
n
80
HIS
80
A
SER
81
n
81
SER
81
A
MET
82
n
82
MET
82
A
LYS
83
n
83
LYS
83
A
ASP
84
n
84
ASP
84
A
VAL
85
n
85
VAL
85
A
PRO
86
n
86
PRO
86
A
VAL
87
n
87
VAL
87
A
GLU
88
n
88
GLU
88
A
PHE
89
n
89
PHE
89
A
PRO
90
n
90
PRO
90
A
GLN
91
n
91
GLN
91
A
GLY
92
n
92
GLY
92
A
LEU
93
n
93
LEU
93
A
GLY
94
n
94
GLY
94
A
LEU
95
n
95
LEU
95
A
VAL
96
n
96
VAL
96
A
THR
97
n
97
THR
97
A
ILE
98
n
98
ILE
98
A
CYS
99
n
99
CYS
99
A
GLU
100
n
100
GLU
100
A
ARG
101
n
101
ARG
101
A
GLU
102
n
102
GLU
102
A
ASP
103
n
103
ASP
103
A
PRO
104
n
104
PRO
104
A
ARG
105
n
105
ARG
105
A
ASP
106
n
106
ASP
106
A
ALA
107
n
107
ALA
107
A
PHE
108
n
108
PHE
108
A
VAL
109
n
109
VAL
109
A
SER
110
n
110
SER
110
A
ASN
111
n
111
ASN
111
A
ASN
112
n
112
ASN
112
A
TYR
113
n
113
TYR
113
A
ASP
114
n
114
ASP
114
A
SER
115
n
115
SER
115
A
LEU
116
n
116
LEU
116
A
ASP
117
n
117
ASP
117
A
ALA
118
n
118
ALA
118
A
LEU
119
n
119
LEU
119
A
PRO
120
n
120
PRO
120
A
ALA
121
n
121
ALA
121
A
GLY
122
n
122
GLY
122
A
SER
123
n
123
SER
123
A
ILE
124
n
124
ILE
124
A
VAL
125
n
125
VAL
125
A
GLY
126
n
126
GLY
126
A
THR
127
n
127
THR
127
A
SER
128
n
128
SER
128
A
SER
129
n
129
SER
129
A
LEU
130
n
130
LEU
130
A
ARG
131
n
131
ARG
131
A
ARG
132
n
132
ARG
132
A
GLN
133
n
133
GLN
133
A
CYS
134
n
134
CYS
134
A
GLN
135
n
135
GLN
135
A
LEU
136
n
136
LEU
136
A
ALA
137
n
137
ALA
137
A
GLU
138
n
138
GLU
138
A
ARG
139
n
139
ARG
139
A
ARG
140
n
140
ARG
140
A
PRO
141
n
141
PRO
141
A
ASP
142
n
142
ASP
142
A
LEU
143
n
143
LEU
143
A
ILE
144
n
144
ILE
144
A
ILE
145
n
145
ILE
145
A
ARG
146
n
146
ARG
146
A
SER
147
n
147
SER
147
A
LEU
148
n
148
LEU
148
A
ARG
149
n
149
ARG
149
A
GLY
150
n
150
GLY
150
A
ASN
151
n
151
ASN
151
A
VAL
152
n
152
VAL
152
A
GLY
153
n
153
GLY
153
A
THR
154
n
154
THR
154
A
ARG
155
n
155
ARG
155
A
LEU
156
n
156
LEU
156
A
SER
157
n
157
SER
157
A
LYS
158
n
158
LYS
158
A
LEU
159
n
159
LEU
159
A
ASP
160
n
160
ASP
160
A
ASN
161
n
161
ASN
161
A
GLY
162
n
162
GLY
162
A
GLU
163
n
163
GLU
163
A
TYR
164
n
164
TYR
164
A
ASP
165
n
165
ASP
165
A
ALA
166
n
166
ALA
166
A
ILE
167
n
167
ILE
167
A
ILE
168
n
168
ILE
168
A
LEU
169
n
169
LEU
169
A
ALA
170
n
170
ALA
170
A
VAL
171
n
171
VAL
171
A
ALA
172
n
172
ALA
172
A
GLY
173
n
173
GLY
173
A
LEU
174
n
174
LEU
174
A
LYS
175
n
175
LYS
175
A
ARG
176
n
176
ARG
176
A
LEU
177
n
177
LEU
177
A
GLY
178
n
178
GLY
178
A
LEU
179
n
179
LEU
179
A
GLU
180
n
180
GLU
180
A
SER
181
n
181
SER
181
A
ARG
182
n
182
ARG
182
A
ILE
183
n
183
ILE
183
A
ARG
184
n
184
ARG
184
A
ALA
185
n
185
ALA
185
A
ALA
186
n
186
ALA
186
A
LEU
187
n
187
LEU
187
A
PRO
188
n
188
PRO
188
A
PRO
189
n
189
PRO
189
A
GLU
190
n
190
GLU
190
A
ILE
191
n
191
ILE
191
A
SER
192
n
192
SER
192
A
LEU
193
n
193
LEU
193
A
PRO
194
n
194
PRO
194
A
ALA
195
n
195
ALA
195
A
VAL
196
n
196
VAL
196
A
GLY
197
n
197
GLY
197
A
GLN
198
n
198
GLN
198
A
GLY
199
n
199
GLY
199
A
ALA
200
n
200
ALA
200
A
VAL
201
n
201
VAL
201
A
GLY
202
n
202
GLY
202
A
ILE
203
n
203
ILE
203
A
GLU
204
n
204
GLU
204
A
CYS
205
n
205
CYS
205
A
ARG
206
n
206
ARG
206
A
LEU
207
n
207
LEU
207
A
ASP
208
n
208
ASP
208
A
ASP
209
n
209
ASP
209
A
SER
210
n
210
SER
210
A
ARG
211
n
211
ARG
211
A
THR
212
n
212
THR
212
A
ARG
213
n
213
ARG
213
A
GLU
214
n
214
GLU
214
A
LEU
215
n
215
LEU
215
A
LEU
216
n
216
LEU
216
A
ALA
217
n
217
ALA
217
A
ALA
218
n
218
ALA
218
A
LEU
219
n
219
LEU
219
A
ASN
220
n
220
ASN
220
A
HIS
221
n
221
HIS
221
A
HIS
222
n
222
HIS
222
A
GLU
223
n
223
GLU
223
A
THR
224
n
224
THR
224
A
ALA
225
n
225
ALA
225
A
LEU
226
n
226
LEU
226
A
ARG
227
n
227
ARG
227
A
VAL
228
n
228
VAL
228
A
THR
229
n
229
THR
229
A
ALA
230
n
230
ALA
230
A
GLU
231
n
231
GLU
231
A
ARG
232
n
232
ARG
232
A
ALA
233
n
233
ALA
233
A
MET
234
n
234
MET
234
A
ASN
235
n
235
ASN
235
A
THR
236
n
236
THR
236
A
ARG
237
n
237
ARG
237
A
LEU
238
n
238
LEU
238
A
GLU
239
n
239
GLU
239
A
GLY
240
n
240
GLY
240
A
ALA
241
n
241
ALA
241
A
CYS
242
n
242
CYS
242
A
GLN
243
n
243
GLN
243
A
VAL
244
n
244
VAL
244
A
PRO
245
n
245
PRO
245
A
ILE
246
n
246
ILE
246
A
GLY
247
n
247
GLY
247
A
SER
248
n
248
SER
248
A
TYR
249
n
249
TYR
249
A
ALA
250
n
250
ALA
250
A
GLU
251
n
251
GLU
251
A
LEU
252
n
252
LEU
252
A
ILE
253
n
253
ILE
253
A
ASP
254
n
254
ASP
254
A
GLY
255
n
255
GLY
255
A
GLU
256
n
256
GLU
256
A
ILE
257
n
257
ILE
257
A
TRP
258
n
258
TRP
258
A
LEU
259
n
259
LEU
259
A
ARG
260
n
260
ARG
260
A
GLY
261
n
261
GLY
261
A
LEU
262
n
262
LEU
262
A
VAL
263
n
263
VAL
263
A
GLY
264
n
264
GLY
264
A
ALA
265
n
265
ALA
265
A
PRO
266
n
266
PRO
266
A
ASP
267
n
267
ASP
267
A
GLY
268
n
268
GLY
268
A
SER
269
n
269
SER
269
A
GLN
270
n
270
GLN
270
A
ILE
271
n
271
ILE
271
A
ILE
272
n
272
ILE
272
A
ARG
273
n
273
ARG
273
A
GLY
274
n
274
GLY
274
A
GLU
275
n
275
GLU
275
A
ARG
276
n
276
ARG
276
A
ARG
277
n
277
ARG
277
A
GLY
278
n
278
GLY
278
A
ALA
279
n
279
ALA
279
A
PRO
280
n
280
PRO
280
A
GLN
281
n
281
GLN
281
A
ASP
282
n
282
ASP
282
A
ALA
283
n
283
ALA
283
A
GLU
284
n
284
GLU
284
A
GLN
285
n
285
GLN
285
A
MET
286
n
286
MET
286
A
GLY
287
n
287
GLY
287
A
ILE
288
n
288
ILE
288
A
SER
289
n
289
SER
289
A
LEU
290
n
290
LEU
290
A
ALA
291
n
291
ALA
291
A
GLU
292
n
292
GLU
292
A
GLU
293
n
293
GLU
293
A
LEU
294
n
294
LEU
294
A
LEU
295
n
295
LEU
295
A
ASN
296
n
296
ASN
296
A
ASN
297
n
297
ASN
297
A
GLY
298
n
298
GLY
298
A
ALA
299
n
299
ALA
299
A
ARG
300
n
300
ARG
300
A
GLU
301
n
301
GLU
301
A
ILE
302
n
302
ILE
302
A
LEU
303
n
303
LEU
303
A
ALA
304
n
304
ALA
304
A
GLU
305
n
305
GLU
305
A
VAL
306
n
306
VAL
306
A
TYR
307
n
307
TYR
307
A
n
308
308
A
n
309
309
A
n
310
310
A
n
311
311
A
n
312
312
A
n
313
313
A
author_defined_assembly
1
monomeric
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
GLU
37
A
N
GLU
37
A
O
LEU
6
A
O
LEU
6
A
O
ARG
7
A
O
ARG
7
A
N
ILE
77
A
N
ILE
77
A
O
HIS
80
A
O
HIS
80
A
N
GLY
202
A
N
GLY
202
A
O
CYS
205
A
O
CYS
205
A
N
GLY
94
A
N
GLY
94
A
O
ILE
144
A
O
ILE
144
A
N
VAL
125
A
N
VAL
125
A
O
ILE
124
A
O
ILE
124
A
N
ALA
166
A
N
ALA
166
A
N
ALA
166
A
N
ALA
166
A
O
VAL
109
A
O
VAL
109
A
O
ASP
106
A
O
ASP
106
A
N
LEU
187
A
N
LEU
187
A
O
ILE
253
A
O
ILE
253
A
N
GLU
256
A
N
GLU
256
A
N
ALA
265
A
N
ALA
265
A
O
GLN
270
A
O
GLN
270
1
A
CG
ARG
44
A
CG
ARG
44
1
Y
1
A
CD
ARG
44
A
CD
ARG
44
1
Y
1
A
NE
ARG
44
A
NE
ARG
44
1
Y
1
A
CZ
ARG
44
A
CZ
ARG
44
1
Y
1
A
NH1
ARG
44
A
NH1
ARG
44
1
Y
1
A
NH2
ARG
44
A
NH2
ARG
44
1
Y
1
A
CG
LYS
59
A
CG
LYS
59
1
Y
1
A
CD
LYS
59
A
CD
LYS
59
1
Y
1
A
CE
LYS
59
A
CE
LYS
59
1
Y
1
A
NZ
LYS
59
A
NZ
LYS
59
1
Y
1
A
CG
LEU
61
A
CG
LEU
61
1
Y
1
A
CD1
LEU
61
A
CD1
LEU
61
1
Y
1
A
CD2
LEU
61
A
CD2
LEU
61
1
Y
1
A
CB
ALA
241
A
CB
ALA
241
1
Y
1
A
MET
1
A
MET
1
1
Y
1
A
LEU
2
A
LEU
2
1
Y
1
A
LEU
49
A
LEU
49
1
Y
1
A
ASP
50
A
ASP
50
1
Y
1
A
THR
51
A
THR
51
1
Y
1
A
PRO
52
A
PRO
52
1
Y
1
A
LEU
53
A
LEU
53
1
Y
1
A
ALA
54
A
ALA
54
1
Y
1
A
LYS
55
A
LYS
55
1
Y
1
A
VAL
56
A
VAL
56
1
Y
1
A
GLY
57
A
GLY
57
1
Y
1
A
ASN
308
A
ASN
308
1
Y
1
A
GLY
309
A
GLY
309
1
Y
1
A
ASP
310
A
ASP
310
1
Y
1
A
ALA
311
A
ALA
311
1
Y
1
A
PRO
312
A
PRO
312
1
Y
1
A
ALA
313
A
ALA
313
1
Y
1
A
PRO
245
10.16
1
-7.97
0.50
120.30
112.33
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
11
11
11
N
1
-14.74
1.70
113.30
98.56
A
A
A
CA
CB
CG
MET
MET
MET
28
28
28
N
1
-14.05
1.60
100.20
86.15
A
A
A
CG
SD
CE
MET
MET
MET
28
28
28
N
1
12.09
1.80
110.60
122.69
A
A
A
N
CA
CB
LYS
LYS
LYS
59
59
59
N
1
7.48
0.50
120.30
127.78
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
74
74
74
N
1
-3.96
0.50
120.30
116.34
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
74
74
74
N
1
10.22
0.90
118.30
128.52
A
A
A
CB
CG
OD1
ASP
ASP
ASP
84
84
84
N
1
-7.44
0.90
118.30
110.86
A
A
A
CB
CG
OD2
ASP
ASP
ASP
84
84
84
N
1
15.38
1.20
123.30
138.68
A
A
A
OE1
CD
OE2
GLU
GLU
GLU
88
88
88
N
1
-13.44
2.00
118.30
104.86
A
A
A
CG
CD
OE1
GLU
GLU
GLU
88
88
88
N
1
-11.27
1.80
110.60
99.33
A
A
A
N
CA
CB
GLN
GLN
GLN
91
91
91
N
1
7.33
0.90
118.30
125.63
A
A
A
CB
CG
OD1
ASP
ASP
ASP
103
103
103
N
1
-5.82
0.90
118.30
112.48
A
A
A
CB
CG
OD2
ASP
ASP
ASP
103
103
103
N
1
3.38
0.50
120.30
123.68
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
105
105
105
N
1
6.61
0.90
118.30
124.91
A
A
A
CB
CG
OD1
ASP
ASP
ASP
106
106
106
N
1
-5.50
0.90
118.30
112.80
A
A
A
CB
CG
OD2
ASP
ASP
ASP
106
106
106
N
1
-3.65
0.60
121.00
117.35
A
A
A
CB
CG
CD1
TYR
TYR
TYR
113
113
113
N
1
6.00
0.90
118.30
124.30
A
A
A
CB
CG
OD1
ASP
ASP
ASP
114
114
114
N
1
5.90
0.50
120.30
126.20
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
131
131
131
N
1
-4.79
0.50
120.30
115.51
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
132
132
132
N
1
-3.24
0.50
120.30
117.06
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
139
139
139
N
1
3.02
0.50
120.30
123.32
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
149
149
149
N
1
5.14
0.50
120.30
125.44
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
155
155
155
N
1
7.89
0.90
118.30
126.19
A
A
A
CB
CG
OD1
ASP
ASP
ASP
160
160
160
N
1
-5.54
0.90
118.30
112.76
A
A
A
CB
CG
OD2
ASP
ASP
ASP
160
160
160
N
1
6.90
0.60
121.00
127.90
A
A
A
CB
CG
CD1
TYR
TYR
TYR
164
164
164
N
1
7.85
0.80
121.30
129.15
A
A
A
CG
CD1
CE1
TYR
TYR
TYR
164
164
164
N
1
7.50
0.90
119.80
127.30
A
A
A
CZ
CE2
CD2
TYR
TYR
TYR
164
164
164
N
1
-5.64
0.50
120.30
114.66
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
176
176
176
N
1
7.81
0.50
120.30
128.11
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
182
182
182
N
1
-9.77
0.50
120.30
110.53
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
182
182
182
N
1
-3.07
0.50
120.30
117.23
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
184
184
184
N
1
-4.80
0.50
120.30
115.50
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
206
206
206
N
1
8.90
1.40
123.60
132.50
A
A
A
CD
NE
CZ
ARG
ARG
ARG
211
211
211
N
1
-3.04
0.50
120.30
117.26
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
213
213
213
N
1
7.95
1.20
123.30
131.25
A
A
A
OE1
CD
OE2
GLU
GLU
GLU
223
223
223
N
1
9.66
1.40
123.60
133.26
A
A
A
CD
NE
CZ
ARG
ARG
ARG
232
232
232
N
1
10.45
1.70
113.30
123.75
A
A
A
CA
CB
CG
MET
MET
MET
234
234
234
N
1
16.50
2.30
121.90
138.40
A
A
A
OD1
CG
ND2
ASN
ASN
ASN
235
235
235
N
1
-6.94
1.10
119.40
112.46
A
A
A
NH1
CZ
NH2
ARG
ARG
ARG
237
237
237
N
1
8.25
0.50
120.30
128.55
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
237
237
237
N
1
10.97
1.20
123.30
134.27
A
A
A
OE1
CD
OE2
GLU
GLU
GLU
251
251
251
N
1
-3.59
0.50
120.30
116.71
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
276
276
276
N
1
4.72
0.50
120.30
125.02
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
276
276
276
N
1
-8.45
1.40
123.60
115.15
A
A
A
CD
NE
CZ
ARG
ARG
ARG
277
277
277
N
1
-6.79
0.50
120.30
113.51
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
277
277
277
N
1
6.20
0.50
120.30
126.50
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
277
277
277
N
1
15.44
2.30
121.90
137.34
A
A
A
OD1
CG
ND2
ASN
ASN
ASN
297
297
297
N
1
-13.91
2.00
121.60
107.69
A
A
A
CB
CG
OD1
ASN
ASN
ASN
297
297
297
N
1
13.83
2.20
113.40
127.23
A
A
A
CA
CB
CG
GLU
GLU
GLU
305
305
305
N
1
13.61
1.90
113.40
127.01
A
A
A
CA
CB
CG
TYR
TYR
TYR
307
307
307
N
1
A
A
O
O
HOH
HOH
413
506
2.18
1_555
3_546
1
A
LYS
59
-103.63
-160.46
1
A
THR
127
-172.11
139.69
1
A
ALA
241
170.93
-176.21
0.1880000
0.1880000
1.76
1
1.76
249
2527
34
0
2244
0.020
1.87
1.50
2.61
1.80
3.53
2.00
5.30
2.50
model building
X-PLOR
refinement
PROLSQ
refinement
X-PLOR
phasing
X-PLOR
PORPHOBILINOGEN DEAMINASE (E.C.2.5.1.61)
STRUCTURE OF PORPHOBILINOGEN DEAMINASE REVEALS A FLEXIBLE MULTIDOMAIN POLYMERASE WITH A SINGLE CATALYTIC SITE
1
N
N
2
N
N
3
N
N
4
N
N
A
PRO
14
A
PRO
14
HELX_P
A
SER
30
A
SER
30
1
1-1
17
A
ARG
44
A
ARG
44
HELX_P
A
VAL
47
A
VAL
47
1
2A1
4
A
LYS
64
A
LYS
64
HELX_P
A
LEU
71
A
LEU
71
1
2-1
8
A
MET
82
A
MET
82
HELX_P
A
ASP
84
A
ASP
84
5
H1
3
A
LEU
116
A
LEU
116
HELX_P
A
ALA
118
A
ALA
118
5
H2
3
A
LEU
130
A
LEU
130
HELX_P
A
ARG
139
A
ARG
139
1
1-2
10
A
VAL
152
A
VAL
152
HELX_P
A
ASP
160
A
ASP
160
1
2-2
9
A
VAL
171
A
VAL
171
HELX_P
A
ARG
176
A
ARG
176
1
3-2
6
A
GLU
180
A
GLU
180
HELX_P
A
ARG
182
A
ARG
182
5
H3
3
A
PRO
189
A
PRO
189
HELX_P
A
ILE
191
A
ILE
191
5
H4
3
A
SER
210
A
SER
210
HELX_P
A
ALA
217
A
ALA
217
1
4-1
8
A
ALA
217
A
ALA
217
HELX_P
A
LEU
219
A
LEU
219
5
H5
3
A
HIS
222
A
HIS
222
HELX_P
A
LEU
238
A
LEU
238
1
1-3
17
A
PRO
280
A
PRO
280
HELX_P
A
PRO
280
A
PRO
280
5
H6
1
A
ALA
283
A
ALA
283
HELX_P
A
ASN
296
A
ASN
296
1
2-3
14
A
ALA
299
A
ALA
299
HELX_P
A
GLU
305
A
GLU
305
1
3-3
7
covale
1.876
none
A
CYS
242
A
SG
CYS
242
1_555
A
DPM
314
B
CHA
DPM
1_555
TRANSFERASE
PORPHYRIN, TRANSFERASE
HEM3_ECOLI
UNP
1
1
P06983
1
313
1PDA
1
313
P06983
A
1
1
313
1
GLY
CONFLICT
ALA
241
1PDA
A
P06983
UNP
241
241
1
ALA
CONFLICT
GLY
261
1PDA
A
P06983
UNP
261
261
5
5
3
parallel
parallel
anti-parallel
anti-parallel
parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
VAL
35
A
VAL
35
A
MET
41
A
MET
41
A
VAL
5
A
VAL
5
A
THR
10
A
THR
10
A
ILE
77
A
ILE
77
A
SER
81
A
SER
81
A
ALA
200
A
ALA
200
A
ARG
206
A
ARG
206
A
LEU
93
A
LEU
93
A
CYS
99
A
CYS
99
A
ILE
144
A
ILE
144
A
ARG
146
A
ARG
146
A
ILE
124
A
ILE
124
A
THR
127
A
THR
127
A
ALA
166
A
ALA
166
A
ALA
170
A
ALA
170
A
ARG
105
A
ARG
105
A
VAL
109
A
VAL
109
A
ALA
185
A
ALA
185
A
LEU
187
A
LEU
187
A
ILE
246
A
ILE
246
A
ILE
253
A
ILE
253
A
GLU
256
A
GLU
256
A
ALA
265
A
ALA
265
A
GLN
270
A
GLN
270
A
GLY
278
A
GLY
278
Unknown
1
BINDING SITE FOR RESIDUE DPM A 314
Software
17
BINDING SITE FOR RESIDUE ACY A 315
Software
5
A
CYS
242
A
CYS
242
1
1_555
A
ARG
11
A
ARG
11
17
1_555
A
SER
13
A
SER
13
17
1_555
A
PHE
62
A
PHE
62
17
1_555
A
LYS
83
A
LYS
83
17
1_555
A
ASP
84
A
ASP
84
17
1_555
A
THR
127
A
THR
127
17
1_555
A
SER
128
A
SER
128
17
1_555
A
SER
129
A
SER
129
17
1_555
A
ARG
131
A
ARG
131
17
1_555
A
ARG
132
A
ARG
132
17
1_555
A
ARG
149
A
ARG
149
17
1_555
A
GLY
150
A
GLY
150
17
1_555
A
ASN
151
A
ASN
151
17
1_555
A
VAL
152
A
VAL
152
17
1_555
A
ARG
155
A
ARG
155
17
1_555
A
CYS
242
A
CYS
242
17
1_555
A
HOH
402
D
HOH
17
1_555
A
LYS
83
A
LYS
83
5
1_555
A
ARG
132
A
ARG
132
5
1_555
A
LEU
169
A
LEU
169
5
1_555
A
ALA
170
A
ALA
170
5
1_555
A
HOH
468
D
HOH
5
1_555
18
P 21 21 2