SMTL ID : 3ve2.1 (4 other biounits)

The 2.1 angstrom crystal structure of Transferrin binding protein B (TbpB) from serogroup B M982 Neisseria meningitidis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

homo-tetramer

Ligands

22 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: Y.20, K.120 Chain D: K.174, R.178 Ligand excluded by PLIP GOL.2: 2 residues within 4Å: Chain A: R.13, V.54 Ligand excluded by PLIP GOL.3: 3 residues within 4Å: Chain A: E.27, K.160, K.304 Ligand excluded by PLIP GOL.4: 5 residues within 4Å: Chain A: N.98, Q.100, K.312, D.315, K.316 Ligand excluded by PLIP GOL.5: 4 residues within 4Å: Chain A: T.94, H.96, K.150, K.314 Ligand excluded by PLIP GOL.13: 4 residues within 4Å: Chain B: Y.20, K.120 Chain C: K.174, R.178 Ligand excluded by PLIP GOL.14: 2 residues within 4Å: Chain B: R.13, V.54 Ligand excluded by PLIP GOL.15: 3 residues within 4Å: Chain B: E.27, K.160, K.304 Ligand excluded by PLIP GOL.16: 5 residues within 4Å: Chain B: N.98, Q.100, K.312, D.315, K.316 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain B: T.94, H.96, K.150, K.314 Ligand excluded by PLIP GOL.25: 5 residues within 4Å: Chain C: T.60, D.61, G.62, D.63, S.64 Ligand excluded by PLIP GOL.26: 7 residues within 4Å: Chain B: P.21, G.22 Chain C: E.24, K.161 Chain D: K.161 Ligands: ACT.32, GOL.34 Ligand excluded by PLIP GOL.27: 5 residues within 4Å: Chain C: R.16, E.59, A.112, S.113, E.114 Ligand excluded by PLIP GOL.28: 3 residues within 4Å: Chain C: R.13, V.54, V.58 Ligand excluded by PLIP GOL.29: 7 residues within 4Å: Chain C: N.98, Q.100, K.312, T.313, K.314, D.315, K.316 Ligand excluded by PLIP GOL.30: 3 residues within 4Å: Chain C: H.96, K.150, K.314 Ligand excluded by PLIP GOL.33: 5 residues within 4Å: Chain D: T.60, D.61, G.62, D.63, S.64 Ligand excluded by PLIP GOL.34: 7 residues within 4Å: Chain A: P.21, G.22 Chain C: K.161 Chain D: E.24, K.161 Ligands: GOL.26, ACT.40 Ligand excluded by PLIP GOL.35: 5 residues within 4Å: Chain D: R.16, E.59, A.112, S.113, E.114 Ligand excluded by PLIP GOL.36: 3 residues within 4Å: Chain D: R.13, V.54, V.58 Ligand excluded by PLIP GOL.37: 7 residues within 4Å: Chain D: N.98, Q.100, K.312, T.313, K.314, D.315, K.316 Ligand excluded by PLIP GOL.38: 3 residues within 4Å: Chain D: H.96, K.150, K.314 Ligand excluded by PLIP

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

SO4.6: 6 residues within 4Å: Chain A: R.17, W.19, E.24, K.161, R.178 Chain D: P.21 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:E.24 Water bridges: A:R.17, A:R.17, A:K.161, A:K.161, A:K.161, A:R.178, C:D.164 Salt bridges: A:R.17, A:K.161, A:K.174, A:R.178 SO4.7: 2 residues within 4Å: Chain A: G.145, K.146 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.146 Water bridges: A:S.144, A:S.144, A:G.145, A:G.145 SO4.8: 3 residues within 4Å: Chain A: W.35, E.36, A.37 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.37 Water bridges: A:D.34, A:W.35, A:R.50 SO4.9: 4 residues within 4Å: Chain A: E.24, E.25, S.26, E.27 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.26, A:S.26, A:E.27 Water bridges: A:E.27 SO4.10: 5 residues within 4Å: Chain A: K.174, R.178 Chain C: T.270 Chain D: Y.20, K.120 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:Y.20, D:Y.20 Salt bridges: D:K.120, A:K.174, A:R.178 Water bridges: A:R.178 SO4.11: 3 residues within 4Å: Chain A: T.42, E.46, K.49 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.42, A:T.42, A:T.42 Water bridges: A:E.46 Salt bridges: A:K.49 SO4.18: 6 residues within 4Å: Chain B: R.17, W.19, E.24, K.161, R.178 Chain C: P.21 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:E.24 Water bridges: B:R.17, B:R.17, B:K.161, B:K.161, B:K.161, B:R.178 Salt bridges: B:R.17, B:K.161, B:K.174, B:R.178 SO4.19: 2 residues within 4Å: Chain B: G.145, K.146 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.146 Water bridges: B:S.144, B:S.144, B:G.145, B:G.145 SO4.20: 3 residues within 4Å: Chain B: W.35, E.36, A.37 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.37 Water bridges: B:W.35, B:R.50 SO4.21: 4 residues within 4Å: Chain B: E.24, E.25, S.26, E.27 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.26, B:S.26, B:E.27 Water bridges: B:E.27 SO4.22: 5 residues within 4Å: Chain B: K.174, R.178 Chain C: Y.20, K.120 Chain D: T.270 7 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: C:Y.20, D:T.270 Water bridges: C:Y.20, B:R.178 Salt bridges: C:K.120, B:K.174, B:R.178 SO4.23: 3 residues within 4Å: Chain B: T.42, E.46, K.49 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.42, B:T.42 Salt bridges: B:K.49 SO4.31: 3 residues within 4Å: Chain C: W.35, E.36, A.37 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.37 SO4.39: 3 residues within 4Å: Chain D: W.35, E.36, A.37 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.37 Water bridges: D:E.36

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

NA.12: 4 residues within 4Å: Chain A: Y.8, G.9, G.39, M.379 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.8, A:G.9, A:G.39 Water bridges: A:G.9, A:R.50 NA.24: 4 residues within 4Å: Chain B: Y.8, G.9, G.39, M.379 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.8, B:G.9, B:G.39 Water bridges: B:G.9, B:R.50

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

ACT.32: 7 residues within 4Å: Chain B: P.21 Chain C: R.17, W.19, E.24, K.174, R.178 Ligands: GOL.26 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:P.21, C:W.19 Water bridges: B:Y.20 Hydrogen bonds: C:E.24 Salt bridges: C:R.17, C:K.161, C:K.174, C:R.178 ACT.40: 7 residues within 4Å: Chain A: P.21 Chain D: R.17, W.19, E.24, K.174, R.178 Ligands: GOL.34 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:W.19, A:P.21 Hydrogen bonds: D:E.24, D:E.24 Water bridges: D:R.178 Salt bridges: D:R.17, D:K.161, D:K.174, D:R.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Calmettes, C. et al., The structural basis of transferrin sequestration by transferrin-binding protein B. Nat.Struct.Mol.Biol. (2012)

Release Date

2012-02-22

Peptides

Transferrin-binding protein 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
A

D
A

Transferrin-binding protein 2

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