SMTL ID : 6vug.1

Diabody bound to a Reverse Transcriptase Aptamer Complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

11 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain B: P.242, R.374, K.382 Chain C: S.35, Y.37 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Salt bridges: B:R.374, B:K.382 Hydrogen bonds: C:S.35, C:Y.37 SO4.2: 4 residues within 4Å: Chain B: Q.238, K.239, E.240 Chain D: R.61 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain B Salt bridges: D:R.61 Hydrogen bonds: B:K.239, B:E.240, B:E.240 SO4.3: 4 residues within 4Å: Chain A: W.410 Chain B: T.378, N.379, K.382 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.378, B:N.379 Salt bridges: B:K.382 SO4.4: 7 residues within 4Å: Chain B: E.210, G.212, Q.213, H.214, R.215 Chain D: T.32, S.33 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:G.212, B:H.214, B:R.215, D:S.33 SO4.5: 4 residues within 4Å: Chain B: E.249, L.250, H.251, W.255 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.249, B:H.251 SO4.6: 3 residues within 4Å: Chain B: A.114, K.117, K.118 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.117, B:K.118 SO4.7: 3 residues within 4Å: Chain B: Q.352, K.369, R.372 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.352 Salt bridges: B:R.372 SO4.8: 3 residues within 4Å: Chain B: S.84, T.85, K.235 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.85, B:T.85 SO4.10: 4 residues within 4Å: Chain C: L.51, Y.54, H.60 Chain D: T.104 No protein-ligand interaction detected (PLIP) SO4.11: 6 residues within 4Å: Chain C: Q.42, K.44, L.52, G.62, P.64, F.67 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.42 Salt bridges: C:K.44 SO4.12: 3 residues within 4Å: Chain C: P.13, S.14, S.15 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.14, C:S.15, C:S.15

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 8 residues within 4Å: Chain B: K.254, W.255, T.256, Y.355, K.366, G.368, K.369, E.394 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.256, B:Y.355, B:K.366

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chesterman, C. et al., Co-crystallization with diabodies: A case study for the introduction of synthetic symmetry. Structure (2021)

Release Date

2021-02-17

Peptides

Reverse transcriptase/ribonuclease H: A
REVERSE TRANSCRIPTASE P51: B
Light chain variable fragment: C
Heavy chain variable fragment: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Reverse transcriptase/ribonuclease H

REVERSE TRANSCRIPTASE P51

Light chain variable fragment

Heavy chain variable fragment

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