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4K4I
Asym. Unit
Info
Asym.Unit (270 KB)
Biol.Unit 1 (71 KB)
Biol.Unit 2 (69 KB)
Biol.Unit 3 (68 KB)
Biol.Unit 4 (70 KB)
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(1)
Title
:
TERNARY CRYSTAL STRUCTURES OF A HUMAN DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND (-)FTC-TP.
Authors
:
R. Vyas, Z. Suo
Date
:
12 Apr 13 (Deposition) - 16 Jul 14 (Release) - 13 Aug 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.25
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Biol. Unit 3: I,J,K,L (1x)
Biol. Unit 4: M,N,O,P (1x)
Keywords
:
Dna Polymerase, Dna Repair, Phosphoryl Transfer Reaction, Transferase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Vyas, W. J. Zahurancik, Z. Suo
Structural Basis For The Binding And Incorporation Of Nucleotide Analogs With L-Stereochemistry By Human Dna Polymerase Lambda.
Proc. Natl. Acad. Sci. Usa V. 111 E3033 2014
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Hetero Components
(4, 35)
Info
All Hetero Components
1a: [[(2R,5S)-5-(4-AZANYL-5-FLUORANYL-... (1RYa)
1b: [[(2R,5S)-5-(4-AZANYL-5-FLUORANYL-... (1RYb)
1c: [[(2R,5S)-5-(4-AZANYL-5-FLUORANYL-... (1RYc)
1d: [[(2R,5S)-5-(4-AZANYL-5-FLUORANYL-... (1RYd)
2a: ACETATE ION (ACTa)
2b: ACETATE ION (ACTb)
2c: ACETATE ION (ACTc)
2d: ACETATE ION (ACTd)
2e: ACETATE ION (ACTe)
2f: ACETATE ION (ACTf)
4a: CACODYLATE ION (CACa)
4b: CACODYLATE ION (CACb)
3a: CALCIUM ION (CAa)
3b: CALCIUM ION (CAb)
3c: CALCIUM ION (CAc)
4d: CALCIUM ION (CAd)
4e: CALCIUM ION (CAe)
4f: CALCIUM ION (CAf)
4g: CALCIUM ION (CAg)
4h: CALCIUM ION (CAh)
4i: CALCIUM ION (CAi)
4j: CALCIUM ION (CAj)
4k: CALCIUM ION (CAk)
4l: CALCIUM ION (CAl)
4m: CALCIUM ION (CAm)
4n: CALCIUM ION (CAn)
4o: CALCIUM ION (CAo)
4p: CALCIUM ION (CAp)
4q: CALCIUM ION (CAq)
4r: CALCIUM ION (CAr)
4s: CALCIUM ION (CAs)
4t: CALCIUM ION (CAt)
4u: CALCIUM ION (CAu)
4v: CALCIUM ION (CAv)
4w: CALCIUM ION (CAw)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1RY
4
Ligand/Ion
[[(2R,5S)-5-(4-AZANYL-5-FLUORANYL-2-OXIDANYLIDENE-PYRIMIDIN-1-YL)-1,3-OXATHIOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE
2
ACT
6
Ligand/Ion
ACETATE ION
3
CA
23
Ligand/Ion
CALCIUM ION
4
CAC
2
Ligand/Ion
CACODYLATE ION
[
close Hetero Component info
]
Sites
(35, 35)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:386 , GLY A:416 , SER A:417 , ARG A:420 , CYS A:425 , GLY A:426 , ASP A:427 , ASP A:429 , TYR A:505 , PHE A:506 , ALA A:510 , ASN A:513 , CA A:605 , CA A:606 , HOH A:702 , HOH A:717 , HOH A:720 , HOH A:736 , HOH A:773 , HOH A:786 , DG B:5 , DC C:6
BINDING SITE FOR RESIDUE 1RY A 601
02
AC2
SOFTWARE
SER A:339 , ILE A:341 , ALA A:344 , HOH A:828 , DA C:5 , HOH C:103
BINDING SITE FOR RESIDUE CA A 602
03
AC3
SOFTWARE
CYS A:300 , ILE A:302 , ILE A:305 , HOH A:822 , DC D:3 , LYS M:307
BINDING SITE FOR RESIDUE CA A 603
04
AC4
SOFTWARE
SER A:463 , HOH A:757 , HOH A:777 , HOH A:796 , HOH A:827 , DT B:10
BINDING SITE FOR RESIDUE CA A 604
05
AC5
SOFTWARE
ASP A:427 , ASP A:429 , 1RY A:601 , HOH A:702
BINDING SITE FOR RESIDUE CA A 605
06
AC6
SOFTWARE
ASP A:427 , ASP A:429 , ASP A:490 , 1RY A:601 , DC C:6
BINDING SITE FOR RESIDUE CA A 606
07
AC7
SOFTWARE
GLU A:396 , GLN A:400 , CYS A:412
BINDING SITE FOR RESIDUE CA A 607
08
AC8
SOFTWARE
LEU A:503 , THR A:555 , GLU A:556 , HOH A:794 , HOH A:799
BINDING SITE FOR RESIDUE ACT A 608
09
AC9
SOFTWARE
HOH B:212 , HOH B:213 , HOH B:220
BINDING SITE FOR RESIDUE CA B 101
10
BC1
SOFTWARE
DG B:2 , DG B:3 , DC N:1
BINDING SITE FOR RESIDUE ACT B 102
11
BC2
SOFTWARE
ARG E:386 , GLY E:416 , SER E:417 , ARG E:420 , CYS E:425 , GLY E:426 , ASP E:427 , ASP E:429 , TYR E:505 , PHE E:506 , ASN E:513 , CA E:602 , CA E:603 , HOH E:733 , HOH E:752 , HOH E:753 , HOH E:754 , HOH E:761 , HOH E:778 , DG F:5 , DC G:6
BINDING SITE FOR RESIDUE 1RY E 601
12
BC3
SOFTWARE
ASP E:427 , ASP E:429 , 1RY E:601 , HOH E:752
BINDING SITE FOR RESIDUE CA E 602
13
BC4
SOFTWARE
ASP E:427 , ASP E:429 , ASP E:490 , 1RY E:601
BINDING SITE FOR RESIDUE CA E 603
14
BC5
SOFTWARE
HOH E:754 , HOH E:778
BINDING SITE FOR RESIDUE CA E 604
15
BC6
SOFTWARE
SER E:339 , ILE E:341 , ALA E:344 , HOH E:726 , DA G:5 , HOH G:101
BINDING SITE FOR RESIDUE CA E 605
16
BC7
SOFTWARE
GLU E:396 , GLN E:400 , CYS E:412 , HOH E:771
BINDING SITE FOR RESIDUE CA E 606
17
BC8
SOFTWARE
SER E:463 , GLU E:465 , HOH E:763 , HOH F:209 , ARG I:441
BINDING SITE FOR RESIDUE CAC E 607
18
BC9
SOFTWARE
THR E:555 , GLU E:556 , HOH E:777
BINDING SITE FOR RESIDUE ACT E 608
19
CC1
SOFTWARE
HOH F:203 , HOH F:205 , HOH F:206 , HOH F:207
BINDING SITE FOR RESIDUE CA F 101
20
CC2
SOFTWARE
DG F:2 , DG F:3
BINDING SITE FOR RESIDUE ACT F 102
21
CC3
SOFTWARE
ARG I:386 , GLY I:416 , SER I:417 , ARG I:420 , GLY I:426 , ASP I:427 , TYR I:505 , SER I:509 , ALA I:510 , ASN I:513 , ARG I:514 , ARG I:517 , CA I:604 , HOH I:752 , HOH I:763 , HOH I:767 , DG J:5 , DC K:6
BINDING SITE FOR RESIDUE 1RY I 601
22
CC4
SOFTWARE
SER I:339 , ILE I:341 , ALA I:344 , HOH I:714 , DA K:5 , HOH K:201
BINDING SITE FOR RESIDUE CA I 602
23
CC5
SOFTWARE
ASP I:427 , ASP I:429 , CA I:604 , HOH I:751 , HOH I:752 , HOH I:756
BINDING SITE FOR RESIDUE CA I 603
24
CC6
SOFTWARE
ASP I:427 , 1RY I:601 , CA I:603 , HOH I:724 , HOH I:752
BINDING SITE FOR RESIDUE CA I 604
25
CC7
SOFTWARE
THR I:555 , GLU I:556
BINDING SITE FOR RESIDUE ACT I 605
26
CC8
SOFTWARE
DC J:4 , DG J:6
BINDING SITE FOR RESIDUE CA J 101
27
CC9
SOFTWARE
HOH J:202
BINDING SITE FOR RESIDUE CA K 101
28
DC1
SOFTWARE
ARG M:386 , GLY M:416 , SER M:417 , ARG M:420 , GLY M:426 , TYR M:505 , SER M:509 , ALA M:510 , ASN M:513 , ARG M:517 , CA M:605 , HOH M:786 , HOH M:801 , HOH M:802 , DG N:5 , DC O:6
BINDING SITE FOR RESIDUE 1RY M 601
29
DC2
SOFTWARE
CYS M:300 , ILE M:302 , PRO M:303 , ILE M:305 , DC P:3
BINDING SITE FOR RESIDUE CA M 602
30
DC3
SOFTWARE
SER M:339 , ILE M:341 , ALA M:344 , DA O:5 , HOH O:101
BINDING SITE FOR RESIDUE CA M 603
31
DC4
SOFTWARE
ASP M:427 , ASP M:429 , CA M:605 , HOH M:787
BINDING SITE FOR RESIDUE CA M 604
32
DC5
SOFTWARE
ASP M:427 , ASP M:429 , 1RY M:601 , CA M:604 , HOH M:786
BINDING SITE FOR RESIDUE CA M 605
33
DC6
SOFTWARE
GLU M:318 , HOH M:800 , HOH M:812 , HOH M:814
BINDING SITE FOR RESIDUE CAC M 606
34
DC7
SOFTWARE
HIS M:290
BINDING SITE FOR RESIDUE ACT M 607
35
DC8
SOFTWARE
HOH M:824 , HOH N:208
BINDING SITE FOR RESIDUE CA N 101
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
View:
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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Sorry, no Info available
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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Atom Selection
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