Interaction between DNA ligase 4 (3w1g_A) and Artemis-derived peptide (3w1g_B)
PDB and SCOP data
PDB ID: 3w1g (all binary interactions in this PDB entry)
Title: Crystal Structure of Human DNA ligase IV-Artemis Complex (Native)
Release date: 2013-04-03
Resolution: 2.5 Å
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Chain A: 3w1g_A
Title: DNA ligase 4
Source organism: Homo sapiens
Number of residues: 610 (27 missing in structure)
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Chain B: 3w1g_B
Title: Artemis-derived peptide
Number of residues: 11 (1 missing in structure)
Structural properties
Hetero-dimer interface properties
Buried interface area: 432.49 Å2
Number of inter-residue contacts at the interface: 33
Number of H-bonds: 2
Experimental structure
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Pairwise interaction
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Biological assembly
Heteromer, 1 protein, 1 peptide.
Interface structure modeling
Residues at the interaction interface
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Interface residues in 3w1g_A
No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, % 1 10 11 V 2.3 100.0 % 2 13 14 H 33.7 33.9 % 3 14 15 V 25.8 100.0 % 4 15 16 P 11.3 18.7 % 5 18 19 D 42.6 60.6 % 6 21 22 S 13.3 26.8 % 7 22 23 T 9.6 66.4 % 8 25 26 R 30.3 21.6 % 9 41 42 E 5.9 6.7 % 10 42 43 F 31.7 98.7 % 11 45 46 S 53.3 86.5 % 12 46 47 W 13.3 100.0 % 13 48 49 K 22.7 14.8 % 14 49 50 F 73.3 100.0 % 15 52 53 A 36.5 50.7 % 16 53 54 L 26.9 58.2 %
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Interface residues in 3w1g_B
No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, % 1 486 2 V 16.0 8.6 % 2 487 3 P 64.6 64.2 % 3 488 4 Q 4.4 6.8 % 4 489 5 W 141.0 91.1 % 5 490 6 E <0.1 0.0 % 6 492 8 F 81.0 60.6 % 7 493 9 F 90.9 83.5 % 8 494 10 K 31.3 20.6 % 9 495 11 R 3.2 2.9 %
Inter-residue contacts at the interaction interface
No. | Residue no. in chain A structure | Residue no. in chain A sequence | Residue in chain A | Residue no. in chain B structure | Residue no. in chain B sequence | Residue in chain B | Contact area, Å2 | Contact type |
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1 | 10 | 11 | V | 489 | 5 | W | 2.3 | |
2 | 13 | 14 | H | 486 | 2 | V | 9.2 | |
3 | 13 | 14 | H | 487 | 3 | P | 3.8 | |
4 | 13 | 14 | H | 488 | 4 | Q | 1.1 | |
5 | 13 | 14 | H | 489 | 5 | W | 19.6 | |
6 | 14 | 15 | V | 489 | 5 | W | 25.8 | |
7 | 15 | 16 | P | 489 | 5 | W | 11.3 | |
8 | 18 | 19 | D | 489 | 5 | W | 14.8 | H-bond |
9 | 18 | 19 | D | 490 | 6 | E | <0.1 | |
10 | 18 | 19 | D | 493 | 9 | F | 27.6 | |
11 | 18 | 19 | D | 494 | 10 | K | 0.2 | |
12 | 21 | 22 | S | 493 | 9 | F | 8.9 | |
13 | 21 | 22 | S | 494 | 10 | K | 4.4 | |
14 | 22 | 23 | T | 493 | 9 | F | 9.6 | |
15 | 25 | 26 | R | 493 | 9 | F | 3.7 | |
16 | 25 | 26 | R | 494 | 10 | K | 26.7 | |
17 | 41 | 42 | E | 493 | 9 | F | 5.9 | |
18 | 42 | 43 | F | 489 | 5 | W | 13.1 | |
19 | 42 | 43 | F | 493 | 9 | F | 18.6 | |
20 | 45 | 46 | S | 489 | 5 | W | 11.7 | |
21 | 45 | 46 | S | 492 | 8 | F | 21.6 | H-bond |
22 | 45 | 46 | S | 493 | 9 | F | 16.7 | |
23 | 45 | 46 | S | 495 | 11 | R | 3.2 | |
24 | 46 | 47 | W | 489 | 5 | W | 13.3 | |
25 | 48 | 49 | K | 492 | 8 | F | 22.7 | |
26 | 49 | 50 | F | 487 | 3 | P | 17.8 | |
27 | 49 | 50 | F | 488 | 4 | Q | 3.3 | |
28 | 49 | 50 | F | 489 | 5 | W | 29.1 | |
29 | 49 | 50 | F | 492 | 8 | F | 23.1 | |
30 | 52 | 53 | A | 487 | 3 | P | 22.9 | |
31 | 52 | 53 | A | 492 | 8 | F | 13.5 | |
32 | 53 | 54 | L | 486 | 2 | V | 6.8 | |
33 | 53 | 54 | L | 487 | 3 | P | 20.1 |
Sequence alignments
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Query protein: sp|P49916|DNLI3_HUMAN DNA ligase 3 OS=Homo sapiens GN=LIG3 PE=1 SV=2
Result domain: 3w1g_A; DNA ligase 4
Alignment data:
Expectation value = 4.02e-38, Score = 155 bits (390),
Identities = 27% (152/572), Positive = 46% (262/572), Gaps = 12% (69/572).
Interface alignment data:
Interface residues in alignment: 0% (0/16).
Identities = 0% (0/0), Positive = 0% (0/0), Gaps = 0% (0/0).
Query: 300 HGDV----YLTVKLLLPGVIK--TVYNLNDKQIVKLFSRIFNCNPD--DMARDLE----- 346
H DV Y ++L+LP + + Y + + + KL+ + N D D + L
3w1g_A: 58 HKDVTDSFYPAMRLILPQLERERMAYGIKETMLAKLYIELLNLPRDGKDALKLLNYRTPT 117
dssp: --------HHHHHHH-HHH----------HHHHHHHHHHHH------HHHHHHH----
Query: 347 --QGDVSE--TIRVFFEQSKSFPPAAKSLLTIQEVDEFLLRLSK---LTKEDEQQQALQD 399
GD + I F + + K LTIQ+V++ L ++ ++D +++L
3w1g_A: 118 GTHGDAGDFAMIAYFVLKPRCL---QKGSLTIQQVNDLLDSIASNNSAKRKDLIKKSLLQ 174
dssp: --HHHHHHHHHHHH-- -----EHHHHHHHHHHHHHHHH---HHHHHHHHHH
Query: 400 IASRCTANDLKCIIRLIKHDLKMNSGAKHVLDALDPNAYEAFKASRNLQDVVERVLHNAQ 459
+ ++ +A + K +IR+I DLK+ + + +A E + +L+ V R LH+
3w1g_A: 175 LITQSSALEQKWLIRMIIKDLKLGVSQQTIFSVFHNDAAELHNVTTDLEKVC-RQLHDPS 233
dssp: HHH---HHHHHHHHHHHH--------HHHHHHHH---HHHHHHH---HHHHH HH-----
Query: 460 EVEKEPGQRRALS-VQASLMTPVQPMLAEACKSVEYAMKKCPNGMFS-EIKYDGERVQVH 517
LS + +L + +PMLA A +E+ K + F E K DGER+Q+H
3w1g_A: 234 ---------VGLSDISITLFSAFKPMLA-AIADIEHIEKDMKHQSFYIETKLDGERMQMH 283
dssp: -----------------EE EE--HHHHHHH-----EEEEE----EEEEEE
Query: 518 KNGDHFSYFSRSLKPVLPHKVAH-----FKDYIPQAFPGGHSM-ILDSEVLLIDNKTGKP 571
K+GD + YFSR+ A +I AF + ILD E++ + T
3w1g_A: 284 KDGDVYKYFSRNGYNYTDQFGASPTEGSLTPFIHNAFKADIQICILDGEMMAYNPNTQTF 343
dssp: EE--EEEEEE----E-HHHH---------HHHHHHHE-----EEEEEEEEEEEE----EE
Query: 572 LPFGT-LGVHKKAAFQDANVCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMVEIPNRIMF 630
+ GT + + D C VFD + N+ L L +R + L IP RI
3w1g_A: 344 MQKGTKFDIKRMVEDSDLQTCYCVFDVLMVNNKKLGHETLRKRYEILSSIFTPIPGRIEI 403
dssp: E-------HHHHHH----EEEEEEEEEEEE--EE-----HHHHHHHHHHHE--E---EEE
Query: 631 SEMKRVTKALDLADMITRVIQEGLEGLVLKDVKGTYEPGKR--HWLKVKKDYLNEGAMAD 688
+ + ++ D + I + EG+++K Y+P KR WLK+K +Y++ + D
3w1g_A: 404 VQKTQAHTKNEVIDALNEAIDKREEGIMVKQPLSIYKPDKRGEGWLKIKPEYVS--GLMD 461
dssp: --EEEE--HHHHHHHHHHHHH-----EEEE----------EEEEEEEE------ --
Query: 689 TADLVVLGAFYGQGSKGGMMSIFLMGCYD---PGSQK--WCTVTKCAGGHDDATLARLQN 743
D++++G ++G+GS+GGMMS FL + PG + + T+++ G T+ L +
3w1g_A: 462 ELDILIVGGYWGKGSRGGMMSHFLCAVAEKPPPGEKPSVFHTLSRVGSG---CTMKELYD 518
dssp: -EEEEEEEEEE---- --EEEEEEEEE---- ---EEEEEEEE-- ---HHHHH
Query: 744 -ELDMVKISK------DPSKIPSWLKVNKIYYPDFIVPDPKKAAVWEITGAEFSKSEAHT 796
L + K K PS I + ++Y +P + + +I AE S+ +
3w1g_A: 519 LGLKLAKYWKPFHRKAPPSSILCGTEKPEVYI------EPCNSVIVQIKAAEIVPSDMYK 572
dssp: HHHHH----EE---------EE-------EE- -HHH--EEEEE--EEEE-----
Query: 797 ADGISIRFPRCTRIRDDKDWKSATNLPQLKEL 828
G ++RFPR +IRDDK+W L L++L
3w1g_A: 573 T-GCTLRFPRIEKIRDDKEWHECMTLDDLEQL 603
dssp: - -EEEE--EEEEEE----HHH--EHHHHHHH