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4K4G
Asym. Unit
Info
Asym.Unit (265 KB)
Biol.Unit 1 (68 KB)
Biol.Unit 2 (67 KB)
Biol.Unit 3 (68 KB)
Biol.Unit 4 (69 KB)
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(1)
Title
:
TERNARY CRYSTAL STRUCTURES OF HUMAN DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND L-DCTP.
Authors
:
R. Vyas, Z. Suo
Date
:
12 Apr 13 (Deposition) - 16 Jul 14 (Release) - 13 Aug 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.15
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, 31)
Info
All Hetero Components
1a: 4-AMINO-1-{2-DEOXY-5-O-[(R)-HYDROX... (1S0a)
1b: 4-AMINO-1-{2-DEOXY-5-O-[(R)-HYDROX... (1S0b)
1c: 4-AMINO-1-{2-DEOXY-5-O-[(R)-HYDROX... (1S0c)
1d: 4-AMINO-1-{2-DEOXY-5-O-[(R)-HYDROX... (1S0d)
2a: ACETATE ION (ACTa)
2b: ACETATE ION (ACTb)
2c: ACETATE ION (ACTc)
2d: ACETATE ION (ACTd)
4a: CACODYLATE ION (CACa)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1S0
4
Ligand/Ion
4-AMINO-1-{2-DEOXY-5-O-[(R)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-L-ERYTHRO-PENTOFURANOSYL}PYRIMIDIN-2(1H)-ONE
2
ACT
4
Ligand/Ion
ACETATE ION
3
CA
22
Ligand/Ion
CALCIUM ION
4
CAC
1
Ligand/Ion
CACODYLATE ION
[
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Sites
(31, 31)
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)
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 , GLY A:508 , ALA A:510 , ASN A:513 , CA A:602 , CA A:603 , HOH A:703 , HOH A:707 , HOH A:720 , HOH A:723 , HOH A:738 , HOH A:773 , HOH A:786 , DG B:5 , DC C:6 , HOH C:102
BINDING SITE FOR RESIDUE 1S0 A 601
02
AC2
SOFTWARE
ASP A:427 , ASP A:429 , 1S0 A:601 , HOH A:703
BINDING SITE FOR RESIDUE CA A 602
03
AC3
SOFTWARE
ASP A:427 , ASP A:429 , ASP A:490 , 1S0 A:601 , HOH A:707 , DC C:6
BINDING SITE FOR RESIDUE CA A 603
04
AC4
SOFTWARE
SER A:339 , ILE A:341 , ALA A:344 , HOH A:812 , DA C:5 , HOH C:101
BINDING SITE FOR RESIDUE CA A 604
05
AC5
SOFTWARE
CYS A:300 , ILE A:302 , ILE A:305 , DC D:3
BINDING SITE FOR RESIDUE CA A 605
06
AC6
SOFTWARE
SER A:463 , HOH A:797 , HOH B:203 , HOH B:210 , HOH B:214 , HOH M:771
BINDING SITE FOR RESIDUE CA A 606
07
AC7
SOFTWARE
HOH B:218 , HOH B:219
BINDING SITE FOR RESIDUE CA B 101
08
AC8
SOFTWARE
DG B:2 , DG B:3 , DC N:1
BINDING SITE FOR RESIDUE ACT B 102
09
AC9
SOFTWARE
ARG E:386 , GLY E:416 , SER E:417 , ARG E:420 , GLY E:426 , ASP E:427 , ASP E:429 , TYR E:505 , PHE E:506 , GLY E:508 , ALA E:510 , ASN E:513 , CA E:602 , CA E:603 , CA E:605 , HOH E:701 , HOH E:736 , HOH E:742 , HOH E:745 , DG F:5 , DC G:6
BINDING SITE FOR RESIDUE 1S0 E 601
10
BC1
SOFTWARE
ASP E:427 , ASP E:429 , 1S0 E:601 , HOH E:701
BINDING SITE FOR RESIDUE CA E 602
11
BC2
SOFTWARE
ASP E:427 , ASP E:429 , ASP E:490 , 1S0 E:601 , HOH E:745 , DC G:6
BINDING SITE FOR RESIDUE CA E 603
12
BC3
SOFTWARE
SER E:463 , GLN E:470 , LYS E:472 , DC F:9
BINDING SITE FOR RESIDUE CA E 604
13
BC4
SOFTWARE
ALA E:510 , 1S0 E:601 , HOH E:742
BINDING SITE FOR RESIDUE CA E 605
14
BC5
SOFTWARE
SER E:339 , ILE E:341 , ALA E:344 , HOH E:729 , DA G:5 , HOH G:102
BINDING SITE FOR RESIDUE CA E 606
15
BC6
SOFTWARE
HOH F:203 , HOH F:205
BINDING SITE FOR RESIDUE CA F 101
16
BC7
SOFTWARE
DG F:2 , DG H:4
BINDING SITE FOR RESIDUE ACT F 102
17
BC8
SOFTWARE
ARG I:386 , SER I:417 , ARG I:420 , GLY I:426 , ASP I:427 , ASP I:429 , TYR I:505 , PHE I:506 , SER I:509 , ALA I:510 , ASN I:513 , ARG I:514 , ARG I:517 , CA I:603 , HOH I:720 , HOH I:741 , HOH I:750 , DG J:5 , DC K:6
BINDING SITE FOR RESIDUE 1S0 I 601
18
BC9
SOFTWARE
ASP I:427 , ASP I:429 , ASP I:490 , CA I:603 , HOH I:719 , HOH I:736
BINDING SITE FOR RESIDUE CA I 602
19
CC1
SOFTWARE
ASP I:427 , ASP I:429 , 1S0 I:601 , CA I:602 , HOH I:736 , HOH I:741 , HOH I:750
BINDING SITE FOR RESIDUE CA I 603
20
CC2
SOFTWARE
SER I:339 , ILE I:341 , ALA I:344 , DA K:5 , HOH K:102 , HOH K:103
BINDING SITE FOR RESIDUE CA I 604
21
CC3
SOFTWARE
PRO I:554 , THR I:555 , GLU I:556
BINDING SITE FOR RESIDUE ACT I 605
22
CC4
SOFTWARE
DC J:4 , DG J:6
BINDING SITE FOR RESIDUE CA J 101
23
CC5
SOFTWARE
HOH A:701 , HOH J:202 , HOH K:101
BINDING SITE FOR RESIDUE CA J 102
24
CC6
SOFTWARE
ARG I:308 , HOH I:766 , DG L:1
BINDING SITE FOR RESIDUE CA L 101
25
CC7
SOFTWARE
GLU M:466 , DC N:9
BINDING SITE FOR RESIDUE ACT M 601
26
CC8
SOFTWARE
ARG M:386 , SER M:417 , ARG M:420 , GLY M:426 , ASP M:427 , TYR M:505 , PHE M:506 , SER M:509 , ALA M:510 , ASN M:513 , ARG M:517 , CA M:603 , HOH M:731 , HOH M:791 , DG N:5 , DC O:6
BINDING SITE FOR RESIDUE 1S0 M 602
27
CC9
SOFTWARE
ASP M:427 , ASP M:429 , 1S0 M:602 , HOH M:791 , HOH M:798
BINDING SITE FOR RESIDUE CA M 603
28
DC1
SOFTWARE
CYS M:300 , ILE M:302 , ILE M:305 , DC P:3
BINDING SITE FOR RESIDUE CA M 604
29
DC2
SOFTWARE
SER M:339 , ILE M:341 , ALA M:344 , DA O:5 , HOH O:101
BINDING SITE FOR RESIDUE CA M 605
30
DC3
SOFTWARE
ASP M:427 , ASP M:429 , ASP M:490 , HOH M:760 , HOH M:798
BINDING SITE FOR RESIDUE CA M 606
31
DC4
SOFTWARE
GLU M:318
BINDING SITE FOR RESIDUE CAC M 607
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
View:
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
View:
Label:
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
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View:
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Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
[
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Atom Selection
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)
Protein
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Hetero
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All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
Chain M
Chain N
Chain O
Chain P
Asymmetric Unit 1
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
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set label size to 20 (allowed range: 1-58)
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