SMTL ID : 4mtk.2 (1 other biounit)

Crystal structure of PA0091 VgrG1, the central spike of the Type VI Secretion System

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.32 Å

Oligo State

homo-trimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: R.26, R.76, R.94 Ligand excluded by PLIP SO4.2: 3 residues within 4Å: Chain A: Q.399, N.401, N.403 Ligand excluded by PLIP SO4.3: 3 residues within 4Å: Chain A: Q.214, R.287, R.289 Ligand excluded by PLIP SO4.4: 2 residues within 4Å: Chain A: A.249, A.250 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: R.187, P.189, G.190 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: F.231, R.409, L.436, P.443 Ligand excluded by PLIP SO4.7: 5 residues within 4Å: Chain A: P.189, G.190, G.191, Y.192, A.193 Ligand excluded by PLIP SO4.8: 7 residues within 4Å: Chain A: P.47, L.48, E.49, Q.79 Chain C: M.215, R.217, R.308 Ligand excluded by PLIP SO4.9: 2 residues within 4Å: Chain A: K.417 Chain B: R.472 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain A: R.502, N.503 Chain C: N.510, D.511 Ligand excluded by PLIP SO4.11: 7 residues within 4Å: Chain A: M.215, R.217, R.308 Chain B: P.47, L.48, E.49, Q.79 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain A: R.107, H.397 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain A: I.108, Q.112, Q.120 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain A: E.218, Q.220 Chain B: R.102 Ligand excluded by PLIP SO4.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain A: R.302, R.313, E.314 Ligand excluded by PLIP SO4.17: 1 residues within 4Å: Chain A: R.531 Ligand excluded by PLIP SO4.18: 1 residues within 4Å: Chain A: R.502 Ligand excluded by PLIP SO4.19: 2 residues within 4Å: Chain A: K.119, R.123 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain A: R.233, A.236, R.237, S.265 Ligand excluded by PLIP SO4.21: 1 residues within 4Å: Chain A: R.187 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain A: R.241, S.242, N.243, R.273 Ligand excluded by PLIP SO4.23: 1 residues within 4Å: Chain A: K.623 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain A: R.139, W.141, E.142, Y.143 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain A: E.142, Q.232, R.387 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain A: T.101, R.102 Chain C: I.279 Ligands: SO4.33 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain A: L.62, P.63, R.293 Ligand excluded by PLIP SO4.28: 1 residues within 4Å: Chain A: R.241 Ligand excluded by PLIP SO4.29: 2 residues within 4Å: Chain A: N.481 Chain B: K.491 Ligand excluded by PLIP SO4.30: 5 residues within 4Å: Chain A: E.321, R.323, E.341, S.342, E.343 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain A: S.66, R.67, F.69 Ligand excluded by PLIP SO4.32: 2 residues within 4Å: Chain A: K.389, W.407 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain A: R.102 Chain C: E.218 Ligands: SO4.26 Ligand excluded by PLIP SO4.34: 3 residues within 4Å: Chain A: R.365 Chain C: V.363, R.365 Ligand excluded by PLIP SO4.36: 6 residues within 4Å: Chain A: R.536, R.538 Chain B: R.536, R.538 Chain C: R.536, R.538 Ligand excluded by PLIP SO4.37: 2 residues within 4Å: Chain B: R.26, R.94 Ligand excluded by PLIP SO4.38: 2 residues within 4Å: Chain B: R.287, R.289 Ligand excluded by PLIP SO4.39: 5 residues within 4Å: Chain B: P.189, G.190, G.191, Y.192, A.193 Ligand excluded by PLIP SO4.40: 3 residues within 4Å: Chain B: Q.399, N.401, N.403 Ligand excluded by PLIP SO4.41: 2 residues within 4Å: Chain B: K.389, W.407 Ligand excluded by PLIP SO4.42: 3 residues within 4Å: Chain B: K.417 Chain C: R.472, P.479 Ligand excluded by PLIP SO4.43: 4 residues within 4Å: Chain B: I.108, Q.110, Q.112, Q.120 Ligand excluded by PLIP SO4.44: 2 residues within 4Å: Chain B: K.119, R.123 Ligand excluded by PLIP SO4.45: 1 residues within 4Å: Chain B: R.187 Ligand excluded by PLIP SO4.46: 1 residues within 4Å: Chain B: R.237 Ligand excluded by PLIP SO4.47: 2 residues within 4Å: Chain B: R.241, P.254 Ligand excluded by PLIP SO4.48: 4 residues within 4Å: Chain B: F.231, R.409, L.436, P.443 Ligand excluded by PLIP SO4.49: 1 residues within 4Å: Chain B: R.531 Ligand excluded by PLIP SO4.50: 1 residues within 4Å: Chain B: R.607 Ligand excluded by PLIP SO4.51: 1 residues within 4Å: Chain B: R.502 Ligand excluded by PLIP SO4.52: 3 residues within 4Å: Chain B: R.302, R.313, E.314 Ligand excluded by PLIP SO4.53: 2 residues within 4Å: Chain B: R.67, Q.172 Ligand excluded by PLIP SO4.54: 3 residues within 4Å: Chain B: R.187, P.189, G.190 Ligand excluded by PLIP SO4.55: 4 residues within 4Å: Chain A: N.510, D.511 Chain B: R.502, N.503 Ligand excluded by PLIP SO4.56: 5 residues within 4Å: Chain A: L.255, Y.256, D.257, R.275 Chain B: S.104 Ligand excluded by PLIP SO4.57: 5 residues within 4Å: Chain B: R.139, E.140, W.141, E.142, Y.143 Ligand excluded by PLIP SO4.58: 2 residues within 4Å: Chain B: S.66, R.67 Ligand excluded by PLIP SO4.59: 1 residues within 4Å: Chain B: R.273 Ligand excluded by PLIP SO4.60: 2 residues within 4Å: Chain B: P.63, R.293 Ligand excluded by PLIP SO4.61: 6 residues within 4Å: Chain B: L.255, Y.256, D.257, R.275 Chain C: S.104 Ligands: SO4.64 Ligand excluded by PLIP SO4.62: 4 residues within 4Å: Chain B: N.534, N.535 Chain C: H.526, D.527 Ligand excluded by PLIP SO4.63: 4 residues within 4Å: Chain B: R.241, S.242, N.243, R.273 Ligand excluded by PLIP SO4.64: 5 residues within 4Å: Chain B: P.221, I.279 Chain C: T.101 Ligands: SO4.61, SO4.91 Ligand excluded by PLIP SO4.65: 2 residues within 4Å: Chain B: N.481 Chain C: K.491 Ligand excluded by PLIP SO4.66: 1 residues within 4Å: Chain B: K.376 Ligand excluded by PLIP SO4.67: 6 residues within 4Å: Chain B: R.289, E.321, R.323, E.341, S.342, E.343 Ligand excluded by PLIP SO4.68: 2 residues within 4Å: Chain B: R.107, H.397 Ligand excluded by PLIP SO4.69: 2 residues within 4Å: Chain B: Q.232, R.387 Ligand excluded by PLIP SO4.70: 6 residues within 4Å: Chain A: Q.504, N.506 Chain B: I.498, Q.504, N.506 Chain C: N.506 Ligand excluded by PLIP SO4.71: 3 residues within 4Å: Chain C: R.187, P.189, G.190 Ligand excluded by PLIP SO4.72: 5 residues within 4Å: Chain C: R.139, E.140, W.141, E.142, Y.143 Ligand excluded by PLIP SO4.73: 4 residues within 4Å: Chain B: N.510, D.511 Chain C: R.502, N.503 Ligand excluded by PLIP SO4.74: 1 residues within 4Å: Chain C: R.273 Ligand excluded by PLIP SO4.75: 2 residues within 4Å: Chain C: K.119, R.123 Ligand excluded by PLIP SO4.76: 3 residues within 4Å: Chain C: R.76, R.94 Ligands: SO4.86 Ligand excluded by PLIP SO4.77: 2 residues within 4Å: Chain C: R.287, R.289 Ligand excluded by PLIP SO4.78: 2 residues within 4Å: Chain C: R.107, H.397 Ligand excluded by PLIP SO4.79: 4 residues within 4Å: Chain C: F.231, R.409, L.436, R.442 Ligand excluded by PLIP SO4.80: 2 residues within 4Å: Chain C: K.389, W.407 Ligand excluded by PLIP SO4.81: 6 residues within 4Å: Chain B: R.217, R.308 Chain C: P.47, L.48, E.49, Q.79 Ligand excluded by PLIP SO4.82: 5 residues within 4Å: Chain A: S.104 Chain C: L.255, Y.256, D.257, R.275 Ligand excluded by PLIP SO4.83: 1 residues within 4Å: Chain C: R.237 Ligand excluded by PLIP SO4.84: 3 residues within 4Å: Chain C: R.302, R.313, E.314 Ligand excluded by PLIP SO4.85: 3 residues within 4Å: Chain A: P.461 Chain C: D.383, Q.384 Ligand excluded by PLIP SO4.86: 5 residues within 4Å: Chain C: R.94, W.98, R.102 Ligands: SO4.76, SO4.91 Ligand excluded by PLIP SO4.87: 3 residues within 4Å: Chain C: E.142, Q.232, R.387 Ligand excluded by PLIP SO4.88: 3 residues within 4Å: Chain C: Q.110, Q.112, Q.120 Ligand excluded by PLIP SO4.89: 2 residues within 4Å: Chain C: R.67, Q.172 Ligand excluded by PLIP SO4.90: 2 residues within 4Å: Chain C: R.241, P.254 Ligand excluded by PLIP SO4.91: 6 residues within 4Å: Chain B: E.218, Q.220, Q.282 Chain C: R.102 Ligands: SO4.64, SO4.86 Ligand excluded by PLIP SO4.92: 1 residues within 4Å: Chain C: N.45 Ligand excluded by PLIP SO4.93: 2 residues within 4Å: Chain A: P.638 Chain C: R.531 Ligand excluded by PLIP SO4.94: 1 residues within 4Å: Chain C: Q.384 Ligand excluded by PLIP SO4.95: 3 residues within 4Å: Chain A: A.635, M.636 Chain C: R.531 Ligand excluded by PLIP SO4.96: 1 residues within 4Å: Chain C: R.187 Ligand excluded by PLIP SO4.97: 2 residues within 4Å: Chain B: R.365 Chain C: R.365 Ligand excluded by PLIP SO4.98: 3 residues within 4Å: Chain C: Q.399, N.401, N.403 Ligand excluded by PLIP SO4.99: 4 residues within 4Å: Chain C: D.10, S.57, H.71, K.173 Ligand excluded by PLIP SO4.100: 3 residues within 4Å: Chain C: S.66, R.67, F.69 Ligand excluded by PLIP SO4.101: 3 residues within 4Å: Chain C: L.62, P.63, R.293 Ligand excluded by PLIP SO4.102: 1 residues within 4Å: Chain C: R.502 Ligand excluded by PLIP SO4.103: 1 residues within 4Å: Chain C: D.519 Ligand excluded by PLIP SO4.104: 4 residues within 4Å: Chain C: G.190, G.191, Y.192, A.193 Ligand excluded by PLIP SO4.105: 3 residues within 4Å: Chain A: R.472, P.479 Chain C: K.417 Ligand excluded by PLIP SO4.106: 5 residues within 4Å: Chain C: E.321, R.323, E.341, S.342, E.343 Ligand excluded by PLIP SO4.107: 4 residues within 4Å: Chain C: K.376, Q.399, N.401, E.402 Ligand excluded by PLIP SO4.108: 2 residues within 4Å: Chain A: K.491 Chain C: N.481 Ligand excluded by PLIP SO4.109: 3 residues within 4Å: Chain C: Q.264, S.265, Q.266 Ligand excluded by PLIP SO4.110: 2 residues within 4Å: Chain A: H.526 Chain C: N.534 Ligand excluded by PLIP SO4.111: 2 residues within 4Å: Chain C: R.22, R.323 Ligand excluded by PLIP SO4.112: 3 residues within 4Å: Chain C: P.200, G.203, H.209 Ligand excluded by PLIP SO4.113: 2 residues within 4Å: Chain A: N.599 Chain C: R.607 Ligand excluded by PLIP SO4.114: 7 residues within 4Å: Chain A: R.520, K.522 Chain B: R.520, K.522 Chain C: R.520, K.522, E.528 Ligand excluded by PLIP

1 x TAM: TRIS(HYDROXYETHYL)AMINOMETHANE(Non-covalent)

TAM.35: 5 residues within 4Å: Chain A: G.468, M.469 Chain B: G.468, M.469 Chain C: M.469 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:M.469, C:Q.423

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sycheva, L.V. et al., The conserved architecture of the T6SS central spike complex. To be Published

Release Date

2014-10-01

Peptides

VgrG1: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

VgrG1

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