SMTL ID : 4k2j.1 (5 other biounits)

Decameric ring structure of KSHV (HHV-8) latency-associated nuclear antigen (LANA) DNA binding domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-10-mer

Ligands

9 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 5 residues within 4Å: Chain A: S.77, Y.94, Y.96 Chain B: S.77, Y.94 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.77, B:S.77 Water bridges: A:S.77, A:Y.94 FMT.6: 5 residues within 4Å: Chain C: S.77, C.92, Y.94 Chain D: S.77, Y.94 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:S.77, C:S.77 Water bridges: C:S.77 FMT.7: 7 residues within 4Å: Chain C: Q.25, G.58, K.61, R.110, W.113, A.120, G.121 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.61, C:R.110, C:W.113 Water bridges: C:Q.25, C:R.110 FMT.11: 5 residues within 4Å: Chain E: S.77, C.92, Y.94 Chain F: S.77, Y.94 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:S.77, F:S.77 Water bridges: E:S.77, E:C.78 FMT.12: 7 residues within 4Å: Chain E: G.58, K.61, R.110, W.113, A.120, G.121 Ligands: CL.16 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:K.61, E:R.110, E:G.121 Water bridges: E:D.55, E:D.55 FMT.20: 5 residues within 4Å: Chain G: P.75, S.77, Y.94 Chain H: S.77, Y.94 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:S.77, H:S.77 Water bridges: G:S.77 FMT.25: 6 residues within 4Å: Chain I: K.21, A.22, Q.25, K.61, W.113, A.120 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:Q.25, I:K.61, I:W.113 Water bridges: I:R.110 FMT.30: 5 residues within 4Å: Chain I: S.77, Y.94 Chain J: P.75, S.77, Y.94 3 PLIP interactions: 1 interactions with chain J, 2 interactions with chain I Hydrogen bonds: J:S.77, I:S.77 Water bridges: I:S.77 FMT.31: 6 residues within 4Å: Chain J: G.58, K.61, R.110, W.113, A.120, G.121 4 PLIP interactions: 4 interactions with chain J Hydrogen bonds: J:K.61, J:R.110, J:R.110, J:G.121

23 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 5 residues within 4Å: Chain A: G.58, K.61, R.110, A.120, G.121 Ligand excluded by PLIP CL.3: 5 residues within 4Å: Chain A: Q.107, S.126, I.127 Chain B: K.131, K.132 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain A: K.131, K.132 Chain B: Q.107, S.126, I.127 Ligand excluded by PLIP CL.5: 6 residues within 4Å: Chain B: R.39, P.41, W.45, Q.98, T.137, Q.138 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain C: Q.107, S.126, I.127 Chain D: K.131, K.132 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain C: R.39, W.45, Q.98, T.137 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain C: K.131, K.132 Chain D: Q.107, S.126, I.127 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain E: Q.107, S.126, I.127 Chain F: K.131, K.132 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain E: Q.6, K.60, P.75, V.76 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain E: H.117, P.118, L.119 Ligand excluded by PLIP CL.16: 6 residues within 4Å: Chain E: Q.25, G.58, K.61, L.62, R.110 Ligands: FMT.12 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain E: K.131, K.132 Chain F: Q.107, S.126, I.127 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain F: P.9, V.10, Q.64 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain F: G.58, R.110, A.120, G.121 Ligand excluded by PLIP CL.21: 5 residues within 4Å: Chain G: Q.107, S.126, I.127 Chain H: K.131, K.132 Ligand excluded by PLIP CL.22: 5 residues within 4Å: Chain G: K.131, K.132 Chain H: Q.107, S.126, I.127 Ligand excluded by PLIP CL.23: 5 residues within 4Å: Chain H: R.39, P.41, W.45, Q.98, T.137 Ligand excluded by PLIP CL.24: 5 residues within 4Å: Chain H: G.58, K.61, R.110, A.120, G.121 Ligand excluded by PLIP CL.26: 5 residues within 4Å: Chain I: K.131, K.132 Chain J: Q.107, S.126, I.127 Ligand excluded by PLIP CL.27: 5 residues within 4Å: Chain I: Q.107, S.126, I.127 Chain J: K.131, K.132 Ligand excluded by PLIP CL.28: 6 residues within 4Å: Chain I: R.13, R.39, G.69, K.72 Chain J: G.83, P.84 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain I: H.117, P.118, L.119 Ligand excluded by PLIP CL.32: 4 residues within 4Å: Chain I: Y.57 Chain J: H.2, R.4, Y.5 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Domsic, J.F. et al., Molecular Basis for Oligomeric-DNA Binding and Episome Maintenance by KSHV LANA. Plos Pathog. (2013)

Release Date

2013-11-06

Peptides

KSHV (HHV-8) latency-associated nuclear antigen (LANA): ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

KSHV (HHV-8) latency-associated nuclear antigen (LANA)

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