SMTL ID : 3qrg.1

Crystal structure of antiRSVF Fab B21m

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-mer

Ligands

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 11 residues within 4Å: Chain A: Q.164, S.166, S.180, S.181, T.182 Chain B: F.173, P.174, V.176, S.184, L.185, S.186 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.166, A:T.182, B:F.173, B:S.184, B:S.186, B:S.186 GOL.2: 9 residues within 4Å: Chain A: Q.41, K.43, K.49, L.51, P.63, F.66, E.85, D.86 Ligands: SO4.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.41, A:K.43, A:K.49, A:E.85 GOL.3: 3 residues within 4Å: Chain A: Y.31, I.96 Chain B: F.103 No protein-ligand interaction detected (PLIP) GOL.4: 8 residues within 4Å: Chain A: V.89, Y.91, Q.104, G.105, K.107 Chain B: G.44, K.45, A.46 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.104, B:G.44 GOL.5: 6 residues within 4Å: Chain A: V.3, M.4, T.5, F.102, Q.104 Ligands: SO4.11 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:M.4 Water bridges: A:M.4, A:D.9, A:D.9, A:Q.104, A:Q.104 GOL.6: 4 residues within 4Å: Chain A: Y.53, A.54, N.57 Chain B: T.104 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:Y.105 Hydrogen bonds: A:N.57 GOL.13: 3 residues within 4Å: Chain B: Y.101, G.102, Y.105 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.101 Water bridges: B:S.32 GOL.14: 6 residues within 4Å: Chain B: I.2, F.27, M.34, R.99, Y.101, Y.109 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.99, B:R.99, B:Y.109 Water bridges: B:G.26 GOL.15: 4 residues within 4Å: Chain A: K.173 Chain B: T.167, S.168, G.169 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.169 Water bridges: B:V.170

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

SO4.7: 5 residues within 4Å: Chain A: Q.41, K.43, Q.46, K.49 Ligands: GOL.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.41, A:Q.46 Water bridges: A:K.43, A:Q.46 Salt bridges: A:K.43, A:K.49 SO4.8: 3 residues within 4Å: Chain A: S.118, N.142 Ligands: SO4.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.118, A:S.118, A:N.142 SO4.9: 3 residues within 4Å: Chain A: P.8, D.9, S.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.9, A:D.9, A:S.10 Water bridges: A:S.10 SO4.10: 4 residues within 4Å: Chain A: V.13, S.14, E.17, K.111 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.14, A:S.14 Water bridges: A:E.17, A:E.17, A:K.111 Salt bridges: A:K.111 SO4.11: 5 residues within 4Å: Chain A: D.1, I.2, V.3, T.101 Ligands: GOL.5 2 PLIP interactions: 2 interactions with chain A Water bridges: A:M.4, A:F.102 SO4.12: 3 residues within 4Å: Chain A: S.10, L.11, A.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.10, A:A.12, A:A.12 SO4.16: 5 residues within 4Å: Chain B: S.139, G.140, G.141, T.142 Ligands: SO4.8 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:S.118, A:S.118 Hydrogen bonds: B:G.141, B:T.142 SO4.17: 3 residues within 4Å: Chain B: Q.1, I.2, Y.109 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.2, B:Y.109 SO4.18: 3 residues within 4Å: Chain B: K.124, G.125, S.210 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.125 Water bridges: B:G.125, B:T.212 SO4.19: 3 residues within 4Å: Chain B: K.73, D.74, T.75 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.73, B:T.75 Water bridges: B:S.30, B:K.73 Salt bridges: B:K.73 SO4.20: 4 residues within 4Å: Chain B: P.9, T.10, K.208, P.209 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.10, B:T.10 Water bridges: B:T.10, B:T.10 SO4.21: 3 residues within 4Å: Chain B: S.67, R.68, N.86 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.67, B:N.86 SO4.22: 3 residues within 4Å: Chain B: S.28, S.30, T.75 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.29, B:S.30, B:S.30, B:T.75 Water bridges: B:S.28 SO4.23: 4 residues within 4Å: Chain B: S.25, G.26, F.27, N.78 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.26, B:F.27, B:N.78

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.24: 8 residues within 4Å: Chain B: E.155, P.156, V.157, T.172, F.173, P.174, A.175, L.185 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.157, B:A.175 Water bridges: B:V.157 Salt bridges: B:E.155

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luo, J. et al., Crystal structure anti-RSV Fab B21m. To be Published

Release Date

2011-08-10

Peptides

Fab light chain: A
Fab heavy chain Fd fragment: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

Fab light chain

Fab heavy chain Fd fragment