SMTL ID : 8sfx.1 (1 other biounit)

High Affinity nanobodies against GFP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-mer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: Y.150, N.197, H.198, Y.199, G.227 Ligands: MLT.3 No protein-ligand interaction detected (PLIP) GOL.2: 6 residues within 4Å: Chain A: F.98, F.99, K.100, D.101, D.102 Ligands: NA.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.101, A:D.101, A:D.101 GOL.10: 4 residues within 4Å: Chain B: Q.40, E.45, R.46, R.109 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.40, B:R.109, B:R.109 Water bridges: B:R.46

1 x MLT: D-MALATE(Non-functional Binders)

MLT.3: 1 residues within 4Å: Ligands: GOL.1 No protein-ligand interaction detected (PLIP)

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

NA.4: 7 residues within 4Å: Chain A: T.60, L.61, V.62, T.63, T.64, I.97, H.180 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.63, A:T.63, A:T.63, A:T.64 Water bridges: A:V.62 NA.5: 6 residues within 4Å: Chain A: F.98, F.99, D.102, G.103, N.104 Ligands: GOL.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.99, A:D.102 NA.6: 4 residues within 4Å: Chain A: P.57, W.58, P.59, Y.142 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.58 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.11: 5 residues within 4Å: Chain B: R.109, A.110, Y.112, W.115 Ligands: PO4.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.112, B:W.115 NA.12: 4 residues within 4Å: Chain A: N.211 Chain B: S.108, R.109, A.110 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.211, B:A.110 Water bridges: B:R.109 NA.13: 4 residues within 4Å: Chain B: R.68, L.69, M.84, L.87 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.68, B:Y.95

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 3 residues within 4Å: Chain A: R.72, P.74, D.75 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.75 Water bridges: A:H.76 Salt bridges: A:R.72 PO4.9: 5 residues within 4Å: Chain A: P.14, E.114, G.115, D.116, T.117 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.116, A:T.117, A:T.117 PO4.14: 4 residues within 4Å: Chain B: R.46, R.109, W.115 Ligands: NA.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.115 Salt bridges: B:R.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ketaren, N.E. et al., High Affinity nanobodies against GFP. To Be Published

Release Date

2024-05-22

Peptides

Green fluorescent protein: A
LaG21: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Green fluorescent protein

LaG21

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