SMTL ID : 5ejk.1

Crystal structure of the Rous sarcoma virus intasome

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.80 Å

Oligo State

homo-octamer

Ligands

2 x DC- DT- DT- DC- DT- DT- DT- DC: DNA (5'-D(*CP*TP*TP*CP*TP*CP*TP*C)-3')(Non-covalent)

DC-DT-DT-DC-DT-DT-DT-DC.1: 18 residues within 4Å: Chain A: D.64, D.121, N.122, G.123, I.146, P.147, G.148 Chain I: G.27, A.28, A.29, A.30, G.31, A.32, A.33, G.34, A.35 Chain K: G.21 Ligands: DA-DG-DT-DG-DT-DC-DT-DT.3 7 PLIP interactions: 3 interactions with chain G, 4 interactions with chain A Hydrogen bonds: G:G.245, G:Y.246, G:Y.246, A:T.144, A:I.146, A:Q.151 Hydrophobic interactions: A:T.143 DC-DT-DT-DC-DT-DT-DT-DC.2: 18 residues within 4Å: Chain E: D.64, D.121, N.122, G.123, I.146, P.147, G.148 Chain I: G.21 Chain K: G.27, A.28, A.29, A.30, G.31, A.32, A.33, G.34, A.35 Ligands: DA-DG-DT-DG-DT-DC-DT-DT.4 Protein-ligand interaction information (PLIP) not available

2 x DA- DG- DT- DG- DT- DC- DT- DT: DNA (5'-D(*AP*GP*TP*GP*TP*CP*TP*T)-3')(Non-functional Binders)(Non-covalent)

DA-DG-DT-DG-DT-DC-DT-DT.3: 10 residues within 4Å: Chain I: G.34, A.35, A.36, G.37, A.38, C.39, A.40, C.41, T.42 Ligands: DC-DT-DT-DC-DT-DT-DT-DC.1 Protein-ligand interaction information (PLIP) not available DA-DG-DT-DG-DT-DC-DT-DT.4: 10 residues within 4Å: Chain C: T.144 Chain K: A.35, A.36, G.37, A.38, C.39, A.40, C.41, T.42 Ligands: DC-DT-DT-DC-DT-DT-DT-DC.2 Protein-ligand interaction information (PLIP) not available

8 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: H.9, H.13, C.37, C.40 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.9, A:H.13, A:C.37, A:C.40 ZN.10: 4 residues within 4Å: Chain B: H.9, H.13, C.37, C.40 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.9, B:H.13, B:C.37, B:C.40 ZN.31: 4 residues within 4Å: Chain C: H.9, H.13, C.37, C.40 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.9, C:H.13, C:C.37, C:C.40 ZN.32: 4 residues within 4Å: Chain D: H.9, H.13, C.37, C.40 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.9, D:H.13, D:C.37, D:C.40 ZN.33: 4 residues within 4Å: Chain E: H.9, H.13, C.37, C.40 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.9, E:H.13, E:C.37, E:C.40 ZN.34: 4 residues within 4Å: Chain F: H.9, H.13, C.37, C.40 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.9, F:H.13, F:C.37, F:C.40 ZN.47: 4 residues within 4Å: Chain G: H.9, H.13, C.37, C.40 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.9, G:H.13, G:C.37, G:C.40 ZN.48: 4 residues within 4Å: Chain H: H.9, H.13, C.37, C.40 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:H.9, H:H.13, H:C.37, H:C.40

36 x W: TUNGSTEN ION(Non-functional Binders)(Non-covalent)

W.6: 4 residues within 4Å: Ligands: W.7, W.8, W.9, W.29 Ligand excluded by PLIP W.7: 4 residues within 4Å: Ligands: W.6, W.23, W.29, W.30 Ligand excluded by PLIP W.8: 4 residues within 4Å: Ligands: W.6, W.9, W.23, W.27 Ligand excluded by PLIP W.9: 4 residues within 4Å: Ligands: W.6, W.8, W.25, W.28 Ligand excluded by PLIP W.11: 4 residues within 4Å: Ligands: W.16, W.17, W.19, W.21 Ligand excluded by PLIP W.12: 4 residues within 4Å: Ligands: W.16, W.17, W.18, W.22 Ligand excluded by PLIP W.13: 4 residues within 4Å: Ligands: W.15, W.20, W.21, W.22 Ligand excluded by PLIP W.14: 4 residues within 4Å: Ligands: W.15, W.18, W.19, W.20 Ligand excluded by PLIP W.15: 4 residues within 4Å: Ligands: W.13, W.14, W.18, W.22 Ligand excluded by PLIP W.16: 4 residues within 4Å: Ligands: W.11, W.12, W.21, W.22 Ligand excluded by PLIP W.17: 4 residues within 4Å: Ligands: W.11, W.12, W.18, W.19 Ligand excluded by PLIP W.18: 5 residues within 4Å: Chain B: P.69 Ligands: W.12, W.14, W.15, W.17 Ligand excluded by PLIP W.19: 4 residues within 4Å: Ligands: W.11, W.14, W.17, W.20 Ligand excluded by PLIP W.20: 4 residues within 4Å: Ligands: W.13, W.14, W.19, W.21 Ligand excluded by PLIP W.21: 4 residues within 4Å: Ligands: W.11, W.13, W.16, W.20 Ligand excluded by PLIP W.22: 4 residues within 4Å: Ligands: W.12, W.13, W.15, W.16 Ligand excluded by PLIP W.23: 6 residues within 4Å: Chain A: R.74 Chain B: R.74 Ligands: W.7, W.8, W.27, W.30 Ligand excluded by PLIP W.24: 4 residues within 4Å: Ligands: W.26, W.28, W.29, W.30 Ligand excluded by PLIP W.25: 4 residues within 4Å: Ligands: W.9, W.26, W.27, W.28 Ligand excluded by PLIP W.26: 5 residues within 4Å: Chain B: R.74 Ligands: W.24, W.25, W.27, W.30 Ligand excluded by PLIP W.27: 5 residues within 4Å: Chain B: R.74 Ligands: W.8, W.23, W.25, W.26 Ligand excluded by PLIP W.28: 4 residues within 4Å: Ligands: W.9, W.24, W.25, W.29 Ligand excluded by PLIP W.29: 4 residues within 4Å: Ligands: W.6, W.7, W.24, W.28 Ligand excluded by PLIP W.30: 5 residues within 4Å: Chain B: P.73 Ligands: W.7, W.23, W.24, W.26 Ligand excluded by PLIP W.35: 4 residues within 4Å: Ligands: W.40, W.42, W.44, W.46 Ligand excluded by PLIP W.36: 4 residues within 4Å: Ligands: W.40, W.41, W.45, W.46 Ligand excluded by PLIP W.37: 4 residues within 4Å: Ligands: W.39, W.43, W.44, W.45 Ligand excluded by PLIP W.38: 4 residues within 4Å: Ligands: W.39, W.41, W.42, W.43 Ligand excluded by PLIP W.39: 5 residues within 4Å: Chain F: R.70 Ligands: W.37, W.38, W.41, W.45 Ligand excluded by PLIP W.40: 4 residues within 4Å: Ligands: W.35, W.36, W.41, W.42 Ligand excluded by PLIP W.41: 4 residues within 4Å: Ligands: W.36, W.38, W.39, W.40 Ligand excluded by PLIP W.42: 4 residues within 4Å: Ligands: W.35, W.38, W.40, W.43 Ligand excluded by PLIP W.43: 4 residues within 4Å: Ligands: W.37, W.38, W.42, W.44 Ligand excluded by PLIP W.44: 4 residues within 4Å: Ligands: W.35, W.37, W.43, W.46 Ligand excluded by PLIP W.45: 5 residues within 4Å: Chain F: P.69 Ligands: W.36, W.37, W.39, W.46 Ligand excluded by PLIP W.46: 4 residues within 4Å: Ligands: W.35, W.36, W.44, W.45 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yin, Z. et al., Crystal structure of the Rous sarcoma virus intasome. Nature (2016)

Release Date

2016-02-17

Peptides

Gag-Pro-Pol polyprotein: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Gag-Pro-Pol polyprotein