SMTL ID : 2xi7.1

N-terminal endonuclease domain of La Crosse virus L-protein

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-octamer

Ligands

16 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 6 residues within 4Å: Chain A: H.35, D.80, D.93, Y.94 Ligands: MN.2, XI7.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.35, A:D.80, A:D.93, A:Y.94 MN.2: 4 residues within 4Å: Chain A: D.53, D.80 Ligands: MN.1, XI7.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.53, A:D.80, H2O.5, H2O.5 MN.4: 4 residues within 4Å: Chain B: D.53, D.80 Ligands: MN.5, XI7.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.53, B:D.80, H2O.10, H2O.10 MN.5: 6 residues within 4Å: Chain B: H.35, D.80, D.93, Y.94 Ligands: MN.4, XI7.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.35, B:D.80, B:D.93, B:Y.94 MN.7: 6 residues within 4Å: Chain C: H.35, D.80, D.93, Y.94 Ligands: MN.8, XI7.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.35, C:D.80, C:D.93, C:Y.94 MN.8: 5 residues within 4Å: Chain C: N.52, D.53, D.80 Ligands: MN.7, XI7.9 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.53, C:D.80, H2O.14, H2O.14 MN.10: 6 residues within 4Å: Chain D: H.35, D.80, D.93, Y.94 Ligands: MN.11, XI7.12 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.35, D:D.80, D:D.93, D:Y.94 MN.11: 4 residues within 4Å: Chain D: D.53, D.80 Ligands: MN.10, XI7.12 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.53, D:D.80, H2O.18, H2O.18 MN.13: 6 residues within 4Å: Chain E: H.35, D.80, D.93, Y.94 Ligands: MN.14, XI7.15 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.35, E:D.80, E:D.93, E:Y.94 MN.14: 4 residues within 4Å: Chain E: D.53, D.80 Ligands: MN.13, XI7.15 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.53, E:D.80, H2O.22, H2O.22 MN.16: 4 residues within 4Å: Chain F: D.53, D.80 Ligands: MN.17, XI7.18 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.53, F:D.80, H2O.27, H2O.27 MN.17: 6 residues within 4Å: Chain F: H.35, D.80, D.93, Y.94 Ligands: MN.16, XI7.18 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.35, F:D.80, F:D.93, F:Y.94 MN.19: 6 residues within 4Å: Chain G: H.35, D.80, D.93, Y.94 Ligands: MN.20, XI7.21 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.35, G:D.80, G:D.93, G:Y.94 MN.20: 5 residues within 4Å: Chain G: N.52, D.53, D.80 Ligands: MN.19, XI7.21 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.53, G:D.80, H2O.31, H2O.31 MN.22: 6 residues within 4Å: Chain H: H.35, D.80, D.93, Y.94 Ligands: MN.23, XI7.24 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:H.35, H:D.80, H:D.93, H:Y.94 MN.23: 4 residues within 4Å: Chain H: D.53, D.80 Ligands: MN.22, XI7.24 4 PLIP interactions: 2 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:D.53, H:D.80, H2O.35, H2O.35

8 x XI7: 2-4-DIOXO-4-PHENYLBUTANOIC ACID(Non-covalent)

XI7.3: 8 residues within 4Å: Chain A: H.35, D.53, D.80, D.93, Y.94, K.95 Ligands: MN.1, MN.2 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.95, A:T.106 Salt bridges: A:H.35, A:K.95 XI7.6: 8 residues within 4Å: Chain B: H.35, D.53, D.80, D.93, Y.94, K.95 Ligands: MN.4, MN.5 4 PLIP interactions: 4 interactions with chain B Water bridges: B:N.52, B:K.95 Salt bridges: B:H.35, B:K.95 XI7.9: 9 residues within 4Å: Chain C: M.32, H.35, D.53, D.80, D.93, Y.94, K.95 Ligands: MN.7, MN.8 4 PLIP interactions: 4 interactions with chain C Water bridges: C:N.52, C:K.95 Salt bridges: C:H.35, C:K.95 XI7.12: 9 residues within 4Å: Chain D: M.32, H.35, D.53, D.80, D.93, Y.94, K.95 Ligands: MN.10, MN.11 3 PLIP interactions: 3 interactions with chain D Water bridges: D:K.95 Salt bridges: D:H.35, D:K.95 XI7.15: 8 residues within 4Å: Chain E: H.35, D.53, D.80, D.93, Y.94, K.95 Ligands: MN.13, MN.14 4 PLIP interactions: 4 interactions with chain E Water bridges: E:K.95, E:K.95 Salt bridges: E:H.35, E:K.95 XI7.18: 8 residues within 4Å: Chain F: H.35, D.53, D.80, D.93, Y.94, K.95 Ligands: MN.16, MN.17 4 PLIP interactions: 4 interactions with chain F Water bridges: F:N.52, F:K.95 Salt bridges: F:H.35, F:K.95 XI7.21: 9 residues within 4Å: Chain G: M.32, H.35, D.53, D.80, D.93, Y.94, K.95 Ligands: MN.19, MN.20 4 PLIP interactions: 4 interactions with chain G Water bridges: G:N.52, G:K.95 Salt bridges: G:H.35, G:K.95 XI7.24: 9 residues within 4Å: Chain H: M.32, H.35, D.53, D.80, D.93, Y.94, K.95 Ligands: MN.22, MN.23 4 PLIP interactions: 4 interactions with chain H Water bridges: H:K.95, H:T.106 Salt bridges: H:H.35, H:K.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reguera, J. et al., Bunyaviridae RNA Polymerases (L-Protein) Have an N-Terminal, Influenza-Like Endonuclease Domain, Essential for Viral CAP-Dependent Transcription. Plos Pathog. (2010)

Release Date

2010-10-06

Peptides

RNA POLYMERASE L: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

RNA POLYMERASE L

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