SMTL ID : 8fxj.1

Crystal structure of Fab460

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 11 residues within 4Å: Chain A: Q.159, S.161, S.175, S.176, T.177 Chain B: F.174, P.175, V.177, S.185, L.186, S.187 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:F.174, B:S.187, A:S.161, A:S.176, A:T.177, A:T.177 GOL.9: 9 residues within 4Å: Chain A: W.90, I.93 Chain B: Y.33, H.35, R.50, K.59, S.99, G.101, Y.106 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.35, B:R.50, B:K.59, B:S.99, B:G.101

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 6 residues within 4Å: Chain A: S.30, Y.31, Y.33, W.90, S.91 Chain B: Y.106 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.31, B:Y.106 Hydrogen bonds: A:S.30, A:Y.33, A:Y.33 Water bridges: A:S.91 ACT.10: 4 residues within 4Å: Chain B: V.93, Q.113, G.114, T.116 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.93 Hydrogen bonds: B:Q.113, B:T.116 Water bridges: B:Q.113, B:T.116

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

SO4.3: 6 residues within 4Å: Chain A: G.156, N.157, S.158, Q.159 Chain B: Q.179, S.180 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:S.180, B:S.180, A:N.157, A:Q.159 Water bridges: B:S.181, A:S.158, A:S.158, A:Q.159, A:T.179 SO4.4: 1 residues within 4Å: Chain A: R.210 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.210 SO4.5: 2 residues within 4Å: Chain A: R.18, T.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.20 Salt bridges: A:R.18 SO4.6: 5 residues within 4Å: Chain A: S.120, D.121, E.122 Chain B: P.131, K.222 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Water bridges: B:K.222, B:K.222 Salt bridges: B:K.222 Hydrogen bonds: A:D.121, A:D.121, A:D.121, A:E.122 SO4.7: 3 residues within 4Å: Chain A: S.7, P.8, A.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.9 SO4.11: 5 residues within 4Å: Chain B: Y.33, R.50, D.52, N.55, N.57 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.52, B:N.55, B:N.57 Salt bridges: B:R.50 SO4.12: 2 residues within 4Å: Chain B: S.140, G.141 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.141 Water bridges: B:G.142 SO4.13: 4 residues within 4Å: Chain B: V.2, G.26, F.27, R.98 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.98 Salt bridges: B:R.98 SO4.14: 3 residues within 4Å: Chain B: D.216, K.217, R.218 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.216, B:R.218 Salt bridges: B:K.217 SO4.15: 4 residues within 4Å: Chain B: T.124, K.125, G.126, S.211 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.124, B:G.126 Water bridges: B:K.125 SO4.16: 2 residues within 4Å: Chain A: K.206 Chain B: K.137 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:K.206, B:K.137 Water bridges: B:K.137 SO4.17: 2 residues within 4Å: Chain B: R.40, E.89 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.89 Salt bridges: B:R.40 SO4.18: 4 residues within 4Å: Chain B: P.221, K.222, S.223, C.224 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.223, B:C.224

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 2 residues within 4Å: Chain A: S.41, S.42 Ligand excluded by PLIP CL.19: 5 residues within 4Å: Chain B: Y.153, E.156, P.157, V.158, A.176 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain B: S.123, T.124 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain B: S.7, G.8 Ligand excluded by PLIP CL.22: 1 residues within 4Å: Chain B: S.88 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, K. et al., Inadequate structural constraint on Fab approach rather than paratope elicitation limits HIV-1 MPER vaccine utility. Nat Commun (2023)

Release Date

2023-10-11

Peptides

Fab460, light chain: A
Fab460, heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

Fab460, light chain

Fab460, heavy chain

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