SMTL ID : 9er2.1

PolII-TCR-STK19 structure.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-2-1-1-1-1-mer

Ligands

11 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain C: G.63, C.71, T.73, C.74, C.81, P.82, H.84 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.71, C:C.74, C:C.81, C:H.84 ZN.2: 5 residues within 4Å: Chain C: C.111, F.113, C.114, C.154, C.184 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.111, C:C.114, C:C.154, C:C.184 ZN.4: 6 residues within 4Å: Chain D: C.1112, L.1114, C.1115, C.1130, C.1133, N.1135 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.1112, D:C.1115, D:C.1130, D:C.1133 ZN.5: 5 residues within 4Å: Chain E: C.88, C.90, C.94, E.96, C.97 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.88, E:C.90, E:C.94, E:C.97 ZN.6: 7 residues within 4Å: Chain K: C.17, E.19, C.20, N.22, C.39, N.41, C.42 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.17, K:C.20, K:C.39, K:C.42 ZN.7: 6 residues within 4Å: Chain K: C.86, C.89, H.91, C.114, C.119, H.121 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.86, K:C.89, K:C.114, K:C.119 ZN.8: 6 residues within 4Å: Chain L: C.7, T.9, C.10, R.42, C.44, C.45 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.7, L:C.10, L:C.44, L:C.45 ZN.9: 5 residues within 4Å: Chain N: C.19, C.22, C.36, E.38, C.39 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.19, N:C.22, N:C.36, N:C.39 ZN.10: 7 residues within 4Å: Chain Q: C.567, C.577, R.579, C.585, F.587, H.588 Ligands: ZN.11 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.567, Q:C.577, Q:C.585, Q:H.588 ZN.11: 4 residues within 4Å: Chain Q: C.585, F.587, H.588 Ligands: ZN.10 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.585, Q:F.587, Q:H.588, Q:H.588 ZN.12: 6 residues within 4Å: Chain S: C.7, F.9, C.10, C.31, V.33, C.34 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.7, S:C.10, S:C.31, S:C.34

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: A.14 Chain C: D.495, D.497, D.499 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.495, C:D.497, C:D.499, C:D.499 MG.15: 5 residues within 4Å: Chain T: K.538, T.539, R.950 Ligands: ADP.13, BEF.14 No protein-ligand interaction detected (PLIP)

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.13: 19 residues within 4Å: Chain T: K.506, L.507, F.508, Q.511, M.534, G.535, L.536, G.537, K.538, T.539, I.540, Q.580, E.584, W.588, N.922, R.950, I.951 Ligands: BEF.14, MG.15 12 PLIP interactions: 12 interactions with chain T Hydrogen bonds: T:K.506, T:Q.511, T:G.535, T:G.537, T:K.538, T:T.539, T:T.539, T:Q.580, T:N.922 Salt bridges: T:K.538, T:R.950, T:R.950

1 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.14: 9 residues within 4Å: Chain T: M.534, G.535, K.538, E.647, G.920, R.947, R.950 Ligands: ADP.13, MG.15 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

van den Heuvel, D. et al., STK19 facilitates the clearance of lesion-stalled RNAPII during transcription-coupled DNA repair. Cell (2024)

Release Date

2024-12-04

Peptides

Isoform 1 of Inactive serine/threonine-protein kinase 19: B
DNA-directed RNA polymerase subunit: C
DNA-directed RNA polymerase subunit beta: D
DNA-directed RNA polymerase II subunit RPB3: E
RNA polymerase II subunit D: F
DNA-directed RNA polymerase II subunit E: G
DNA-directed RNA polymerases I, II, and III subunit RPABC2: H
DNA-directed RNA polymerase subunit: I
DNA-directed RNA polymerases I, II, and III subunit RPABC3: J
DNA-directed RNA polymerase II subunit RPB9: K
DNA-directed RNA polymerases I, II, and III subunit RPABC5: L
DNA-directed RNA polymerase II subunit RPB11-a: M
RNA polymerase II subunit K: N
UV-stimulated scaffold protein A: QR
Transcription elongation factor 1 homolog: S
DNA excision repair protein ERCC-6: T
DNA excision repair protein ERCC-8: U
DNA damage-binding protein 1: V

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
Q

C
A

D
B

E
C

F
D

G
E

H
F

I
G

J
H

K
I

L
J

M
K

N
L

Q
c

R
M

S
O

T
b

U
a

V
d

Isoform 1 of Inactive serine/threonine-protein kinase 19

DNA-directed RNA polymerase subunit

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase II subunit RPB3

RNA polymerase II subunit D

DNA-directed RNA polymerase II subunit E

DNA-directed RNA polymerases I, II, and III subunit RPABC2

DNA-directed RNA polymerase subunit

DNA-directed RNA polymerases I, II, and III subunit RPABC3

DNA-directed RNA polymerase II subunit RPB9

DNA-directed RNA polymerases I, II, and III subunit RPABC5

DNA-directed RNA polymerase II subunit RPB11-a

RNA polymerase II subunit K

UV-stimulated scaffold protein A

Transcription elongation factor 1 homolog

DNA excision repair protein ERCC-6

DNA excision repair protein ERCC-8

DNA damage-binding protein 1

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