SMTL ID : 8sfv.1

High affinity nanobodies to GFP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

hetero-1-1-mer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: R.72, P.74, D.75, H.76 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.72 Water bridges: A:D.75 GOL.11: 4 residues within 4Å: Chain B: M.3, A.4, Q.5, R.101 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.5, B:Q.5, B:R.101, B:R.101 GOL.12: 5 residues within 4Å: Chain B: V.16, Q.17, G.19, G.20, S.21 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.21

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

SO4.2: 3 residues within 4Å: Chain A: E.18, R.121 Chain B: Q.103 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.18, B:Q.103 Salt bridges: A:R.121 SO4.3: 3 residues within 4Å: Chain A: F.113, E.114, G.115 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.115 SO4.13: 5 residues within 4Å: Chain A: G.52, K.53, R.214, D.215 Chain B: Y.60 4 PLIP interactions: 4 interactions with chain A Water bridges: A:G.52, A:G.52, A:R.214, A:D.215 SO4.14: 3 residues within 4Å: Chain B: R.54, N.75, Q.103 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.75 Salt bridges: B:R.54 SO4.15: 3 residues within 4Å: Chain B: Q.40, R.46, R.109 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.40, B:Q.40 Salt bridges: B:R.46, B:R.109

11 x NA: SODIUM ION(Non-functional Binders)

NA.4: 8 residues within 4Å: Chain A: T.60, L.61, V.62, T.63, T.64, I.97, Y.105 Ligands: NA.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.63, A:T.63, A:T.64 NA.5: 4 residues within 4Å: Chain A: E.6, K.78, D.81, L.193 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.6, A:E.6 Water bridges: A:E.6 NA.6: 3 residues within 4Å: Chain A: P.55, L.136, H.138 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.55, A:H.138 NA.7: 2 residues within 4Å: Chain A: N.145, R.167 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.145, A:R.167, A:R.167 Water bridges: A:N.169 NA.8: 8 residues within 4Å: Chain A: P.59, T.60, V.62, T.63, Y.144, I.166, H.168 Ligands: NA.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.62, A:T.63, A:T.63, A:Y.144, A:Y.144 NA.9: 5 residues within 4Å: Chain A: X.66, Q.93, A.109, V.111, N.120 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.64, A:N.120 Water bridges: A:Q.93 NA.10: 1 residues within 4Å: Chain A: N.143 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.143 NA.16: 4 residues within 4Å: Chain B: S.53, S.55, T.57, D.58 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.53, B:S.55, B:S.55 Water bridges: B:S.55 NA.17: 4 residues within 4Å: Chain B: P.31, R.54, N.75, N.78 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.54, B:R.54 NA.18: 4 residues within 4Å: Chain B: S.25, T.79, V.80, Y.81 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.25, B:T.79, B:T.79 NA.19: 3 residues within 4Å: Chain B: R.100, R.101, E.113 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.101, B:E.113, B:E.113, B:E.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ketaren, N.E. et al., High affinity nanobodies to GFP. To Be Published

Release Date

2024-05-22

Peptides

Green fluorescent protein: A
LaG19: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Green fluorescent protein

LaG19

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