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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.32 Å

Oligo State

homo-trimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: R.502, N.503 Chain C: N.510, D.511 Ligand excluded by PLIP SO4.2: 3 residues within 4Å: Chain A: R.187, P.189, G.190 Ligand excluded by PLIP SO4.3: 3 residues within 4Å: Chain A: F.231, R.409, L.436 Ligand excluded by PLIP SO4.4: 2 residues within 4Å: Chain A: K.389, W.407 Ligand excluded by PLIP SO4.5: 5 residues within 4Å: Chain A: L.224, D.257, R.275 Chain B: S.104 Ligands: SO4.27 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: Q.399, N.401, N.403 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain A: R.472, P.479 Chain C: K.417 Ligands: SO4.141 Ligand excluded by PLIP SO4.8: 8 residues within 4Å: Chain A: L.46, 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: R.107, H.397 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain A: R.76, R.94 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain A: R.302, R.313, E.314 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain A: R.241, P.254 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain A: I.108, Q.110, Q.112, Q.120 Ligand excluded by PLIP SO4.14: 1 residues within 4Å: Chain A: R.502 Ligand excluded by PLIP SO4.15: 2 residues within 4Å: Chain A: R.365 Chain C: R.365 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain A: R.531 Chain B: P.638 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain A: K.491 Chain C: N.481 Ligand excluded by PLIP SO4.18: 2 residues within 4Å: Chain A: N.599 Chain C: R.607 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain A: N.599, N.601 Chain C: R.607 Ligand excluded by PLIP SO4.20: 1 residues within 4Å: Chain A: R.187 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain A: Q.214, R.287, R.289 Ligand excluded by PLIP SO4.22: 1 residues within 4Å: Chain A: R.207 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: N.534 Chain B: H.526 Ligands: SO4.25, SO4.122 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain A: N.535 Chain C: N.543 Ligands: SO4.24 Ligand excluded by PLIP SO4.26: 1 residues within 4Å: Chain A: R.237 Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain A: P.221, I.279 Chain B: T.101 Ligands: SO4.5 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain A: E.24, G.25, R.26, E.36 Ligand excluded by PLIP SO4.29: 1 residues within 4Å: Chain A: K.621 Ligand excluded by PLIP SO4.30: 2 residues within 4Å: Chain A: K.119, R.123 Ligand excluded by PLIP SO4.31: 5 residues within 4Å: Chain A: S.104 Chain C: L.255, Y.256, D.257, R.275 Ligand excluded by PLIP SO4.32: 1 residues within 4Å: Chain A: K.376 Ligand excluded by PLIP SO4.33: 4 residues within 4Å: Chain A: R.139, W.141, E.142, Y.143 Ligand excluded by PLIP SO4.34: 4 residues within 4Å: Chain A: E.61, L.62, P.63, R.293 Ligand excluded by PLIP SO4.35: 5 residues within 4Å: Chain A: P.189, G.190, G.191, Y.192, A.193 Ligand excluded by PLIP SO4.36: 2 residues within 4Å: Chain A: S.66, R.67 Ligand excluded by PLIP SO4.37: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.38: 4 residues within 4Å: Chain A: A.635, M.636, P.638 Chain C: R.531 Ligand excluded by PLIP SO4.39: 1 residues within 4Å: Chain A: R.486 Ligand excluded by PLIP SO4.40: 2 residues within 4Å: Chain A: Y.197, Y.198 Ligand excluded by PLIP SO4.41: 2 residues within 4Å: Chain A: E.617, D.619 Ligand excluded by PLIP SO4.42: 3 residues within 4Å: Chain A: D.383, Q.384 Chain B: P.461 Ligand excluded by PLIP SO4.43: 3 residues within 4Å: Chain A: E.142, Q.232, R.387 Ligand excluded by PLIP SO4.44: 2 residues within 4Å: Chain A: N.481 Chain B: K.491 Ligand excluded by PLIP SO4.45: 5 residues within 4Å: Chain A: E.321, R.323, E.341, S.342, E.343 Ligand excluded by PLIP SO4.46: 2 residues within 4Å: Chain A: R.67, Q.172 Ligand excluded by PLIP SO4.47: 3 residues within 4Å: Chain A: Q.264, S.265, Q.266 Ligand excluded by PLIP SO4.48: 2 residues within 4Å: Chain A: G.605 Chain B: Y.595 Ligand excluded by PLIP SO4.50: 9 residues within 4Å: Chain A: R.520, K.522, E.528 Chain B: R.520, K.522, E.528 Chain C: R.520, K.522, E.528 Ligand excluded by PLIP SO4.51: 3 residues within 4Å: Chain A: N.510 Chain B: R.502, N.503 Ligand excluded by PLIP SO4.52: 2 residues within 4Å: Chain B: R.187, G.190 Ligand excluded by PLIP SO4.53: 3 residues within 4Å: Chain B: Q.399, N.401, N.403 Ligand excluded by PLIP SO4.54: 2 residues within 4Å: Chain B: K.119, R.123 Ligand excluded by PLIP SO4.55: 2 residues within 4Å: Chain B: R.287, R.289 Ligand excluded by PLIP SO4.56: 4 residues within 4Å: Chain B: F.231, R.409, L.436, R.442 Ligand excluded by PLIP SO4.57: 3 residues within 4Å: Chain B: K.417 Chain C: R.472, P.479 Ligand excluded by PLIP SO4.58: 4 residues within 4Å: Chain B: I.108, Q.110, Q.112, Q.120 Ligand excluded by PLIP SO4.59: 2 residues within 4Å: Chain B: K.389, W.407 Ligand excluded by PLIP SO4.60: 2 residues within 4Å: Chain B: R.76, R.94 Ligand excluded by PLIP SO4.61: 8 residues within 4Å: Chain B: M.215, R.217, R.308 Chain C: L.46, P.47, L.48, E.49, Q.79 Ligand excluded by PLIP SO4.62: 6 residues within 4Å: Chain A: R.217, R.308 Chain B: P.47, L.48, E.49, Q.79 Ligand excluded by PLIP SO4.63: 3 residues within 4Å: Chain A: K.417 Chain B: R.472, P.479 Ligand excluded by PLIP SO4.64: 4 residues within 4Å: Chain B: E.321, R.323, E.341, E.343 Ligand excluded by PLIP SO4.65: 1 residues within 4Å: Chain B: R.187 Ligand excluded by PLIP SO4.66: 3 residues within 4Å: Chain A: L.529 Chain B: D.519, N.521 Ligand excluded by PLIP SO4.67: 4 residues within 4Å: Chain B: R.233, A.236, R.237, S.265 Ligand excluded by PLIP SO4.68: 4 residues within 4Å: Chain B: Y.256, R.275 Chain C: S.104 Ligands: SO4.96 Ligand excluded by PLIP SO4.69: 5 residues within 4Å: Chain B: R.139, E.140, W.141, E.142, Y.143 Ligand excluded by PLIP SO4.70: 2 residues within 4Å: Chain A: E.218 Chain B: R.102 Ligand excluded by PLIP SO4.71: 1 residues within 4Å: Chain B: N.45 Ligand excluded by PLIP SO4.72: 1 residues within 4Å: Chain B: R.502 Ligand excluded by PLIP SO4.73: 2 residues within 4Å: Chain B: N.481 Chain C: K.491 Ligand excluded by PLIP SO4.74: 3 residues within 4Å: Chain A: R.607 Chain B: N.599, N.601 Ligand excluded by PLIP SO4.75: 4 residues within 4Å: Chain A: R.531 Chain B: A.635, M.636, P.638 Ligand excluded by PLIP SO4.76: 2 residues within 4Å: Chain B: R.531 Chain C: P.638 Ligand excluded by PLIP SO4.77: 3 residues within 4Å: Chain B: P.307, R.308, D.309 Ligand excluded by PLIP SO4.78: 2 residues within 4Å: Chain B: R.67, Q.172 Ligand excluded by PLIP SO4.79: 2 residues within 4Å: Chain B: R.107, H.397 Ligand excluded by PLIP SO4.80: 3 residues within 4Å: Chain B: N.534 Chain C: H.526 Ligands: SO4.121 Ligand excluded by PLIP SO4.81: 2 residues within 4Å: Chain A: H.526 Chain B: H.518 Ligand excluded by PLIP SO4.82: 3 residues within 4Å: Chain B: R.302, R.313, E.314 Ligand excluded by PLIP SO4.83: 5 residues within 4Å: Chain B: P.189, G.190, G.191, Y.192, A.193 Ligand excluded by PLIP SO4.84: 2 residues within 4Å: Chain A: R.365 Chain B: R.365 Ligand excluded by PLIP SO4.85: 5 residues within 4Å: Chain B: R.241, S.242, N.243, E.269, R.273 Ligand excluded by PLIP SO4.86: 4 residues within 4Å: Chain A: G.517 Chain B: L.507, V.508, E.509 Ligand excluded by PLIP SO4.87: 2 residues within 4Å: Chain B: S.66, R.67 Ligand excluded by PLIP SO4.88: 3 residues within 4Å: Chain B: L.62, P.63, R.293 Ligand excluded by PLIP SO4.89: 2 residues within 4Å: Chain B: R.241, P.254 Ligand excluded by PLIP SO4.90: 3 residues within 4Å: Chain B: D.383, Q.384 Chain C: P.461 Ligand excluded by PLIP SO4.91: 1 residues within 4Å: Chain B: K.623 Ligand excluded by PLIP SO4.92: 1 residues within 4Å: Chain B: Q.626 Ligand excluded by PLIP SO4.93: 3 residues within 4Å: Chain A: Q.626 Chain B: G.565, A.581 Ligand excluded by PLIP SO4.94: 1 residues within 4Å: Chain B: Y.183 Ligand excluded by PLIP SO4.95: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.96: 4 residues within 4Å: Chain B: P.221, I.279 Chain C: T.101 Ligands: SO4.68 Ligand excluded by PLIP SO4.97: 1 residues within 4Å: Chain B: K.574 Ligand excluded by PLIP SO4.98: 2 residues within 4Å: Chain B: A.249, A.250 Ligand excluded by PLIP SO4.99: 3 residues within 4Å: Chain B: K.376, N.401, E.402 Ligand excluded by PLIP SO4.100: 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 SO4.101: 4 residues within 4Å: Chain B: N.510, D.511 Chain C: R.502, N.503 Ligand excluded by PLIP SO4.102: 3 residues within 4Å: Chain C: Q.399, N.401, N.403 Ligand excluded by PLIP SO4.103: 2 residues within 4Å: Chain C: R.76, R.94 Ligand excluded by PLIP SO4.104: 2 residues within 4Å: Chain C: R.107, H.397 Ligand excluded by PLIP SO4.105: 2 residues within 4Å: Chain A: P.638 Chain C: R.531 Ligand excluded by PLIP SO4.106: 5 residues within 4Å: Chain C: I.108, F.109, Q.110, Q.112, Q.120 Ligand excluded by PLIP SO4.107: 1 residues within 4Å: Chain C: R.502 Ligand excluded by PLIP SO4.108: 3 residues within 4Å: Chain B: R.607 Chain C: N.599, N.601 Ligand excluded by PLIP SO4.109: 4 residues within 4Å: Chain B: E.218, Q.220, Q.282 Chain C: R.102 Ligand excluded by PLIP SO4.110: 1 residues within 4Å: Chain C: R.241 Ligand excluded by PLIP SO4.111: 5 residues within 4Å: Chain C: R.139, E.140, W.141, E.142, Y.143 Ligand excluded by PLIP SO4.112: 1 residues within 4Å: Chain C: R.486 Ligand excluded by PLIP SO4.113: 3 residues within 4Å: Chain B: R.531 Chain C: M.636, P.638 Ligand excluded by PLIP SO4.114: 2 residues within 4Å: Chain B: L.529 Chain C: N.521 Ligand excluded by PLIP SO4.115: 1 residues within 4Å: Chain C: K.376 Ligand excluded by PLIP SO4.116: 2 residues within 4Å: Chain C: R.67, Q.172 Ligand excluded by PLIP SO4.117: 2 residues within 4Å: Chain C: R.187, G.190 Ligand excluded by PLIP SO4.118: 1 residues within 4Å: Chain C: R.187 Ligand excluded by PLIP SO4.119: 3 residues within 4Å: Chain C: E.142, Q.232, R.387 Ligand excluded by PLIP SO4.120: 2 residues within 4Å: Chain C: R.287, R.289 Ligand excluded by PLIP SO4.121: 3 residues within 4Å: Chain A: H.518 Chain C: H.526 Ligands: SO4.80 Ligand excluded by PLIP SO4.122: 3 residues within 4Å: Chain B: H.526 Chain C: H.518 Ligands: SO4.24 Ligand excluded by PLIP SO4.123: 2 residues within 4Å: Chain C: K.119, R.123 Ligand excluded by PLIP SO4.124: 1 residues within 4Å: Chain C: R.237 Ligand excluded by PLIP SO4.125: 4 residues within 4Å: Chain C: F.231, R.409, L.436, P.443 Ligand excluded by PLIP SO4.126: 3 residues within 4Å: Chain A: T.101 Chain C: P.221, I.279 Ligand excluded by PLIP SO4.127: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.128: 2 residues within 4Å: Chain C: K.173, R.174 Ligand excluded by PLIP SO4.129: 3 residues within 4Å: Chain C: L.62, P.63, R.293 Ligand excluded by PLIP SO4.130: 2 residues within 4Å: Chain C: S.66, R.67 Ligand excluded by PLIP SO4.131: 4 residues within 4Å: Chain C: R.241, S.242, N.243, R.273 Ligand excluded by PLIP SO4.132: 3 residues within 4Å: Chain C: Q.264, S.265, Q.266 Ligand excluded by PLIP SO4.133: 3 residues within 4Å: Chain C: R.148, V.363, R.365 Ligand excluded by PLIP SO4.134: 3 residues within 4Å: Chain C: L.507, V.508, E.509 Ligand excluded by PLIP SO4.135: 1 residues within 4Å: Chain C: K.623 Ligand excluded by PLIP SO4.136: 5 residues within 4Å: Chain C: P.189, G.190, G.191, Y.192, A.193 Ligand excluded by PLIP SO4.137: 2 residues within 4Å: Chain C: K.389, W.407 Ligand excluded by PLIP SO4.138: 3 residues within 4Å: Chain C: R.323, S.342, E.343 Ligand excluded by PLIP SO4.139: 1 residues within 4Å: Chain C: R.323 Ligand excluded by PLIP SO4.140: 1 residues within 4Å: Chain C: Q.384 Ligand excluded by PLIP SO4.141: 4 residues within 4Å: Chain A: R.472 Chain C: K.417, W.419 Ligands: SO4.7 Ligand excluded by PLIP SO4.142: 4 residues within 4Å: Chain A: D.527 Chain B: L.542 Chain C: N.534, N.535 Ligand excluded by PLIP SO4.143: 2 residues within 4Å: Chain B: G.605 Chain C: Y.595 Ligand excluded by PLIP SO4.144: 8 residues within 4Å: Chain A: I.498, Q.504, N.506 Chain B: I.498, N.506 Chain C: I.498, Q.504, N.506 Ligand excluded by PLIP

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

TAM.49: 3 residues within 4Å: Chain A: M.469 Chain B: M.469 Chain C: M.469 No protein-ligand interaction detected (PLIP)

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
A

B
B

C
C

VgrG1

Related Entries With Identical Sequence