MolNFT v2 · #155638 · protein
Structure of the phycobilisome from the red alga Porphyridium purpureum
6KGX: “Structure of the phycobilisome from the red alga Porphyridium purpureum”. Electron microscopy at 2.8, 3 ligands (PEB, CYC, PUB). MolNFT v2 #155638 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6KGX
- Type
- protein
- Length
- 125,515 residues
- Chains
- 706
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Porphyridium purpureum
- UniProt
- E2IH77, P11393, W0RZ90, W0RYI4, W0RZB2, W0RYM0, W0S279, W0S1U6, W0RZE2, W0RZJ2
- Ligands
- PEB, CYC, PUB
Structure
electron microscopy · resolution 2.8 · 32 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A1, C1, E1, G1, I1, K1, N1, P1, R1, T1, V1, X1, c1, e1, g1, i1, k1, m1, p1, r1, t1, v1, x1, z1, O2, Q2, S2, U2, W2, Z2, b2, d2, f2, h2, j2, l2, A3, C3, E3, G3, I3, K3, M3, O3, Q3, S3, U3, W3, A4, C4, E4, G4, I4, K4, N4, P4, R4, T4, V4, X4, c4, e4, g4, i4, k4, m4, p4, r4, t4, v4, x4, z4, J5, O6, Q6, S6, U6, W6, Z6, b6, d6, f6, h6, j6, l6, O7, Q7, S7, U7, W7, Z7, b7, d7, f7, h7, j7, l7, C8, E8, G8, I8, K8, M8, O8, Q8, S8, U8, W8, Y8, a8, d8, f8, h8, j8, l8, B9, D9, F9, H9, J9, L9, N9, P9, R9, T9, V9, X9, CA, EA, GA, IA, KA, MA, OA, QA, SA, UA, WA, YA, aA, dA, fA, hA, jA, lA, OB, QB, SB, UB, WB, ZB, bB, dB, fB, hB, jB, lB, JC, AD, CD, ED, GD, ID, KD, MD, OD, QD, SD, UD, WD, AE, CE, EE, GE, IE, KE, ME, OE, QE, SE, UE, WE, YE, aE, cE, eE, gE, iE, kE, mE, oE, qE, sE, uE, OF, QF, SF, UF, WF, ZF, bF, dF, fF, hF, jF, lF, AG, CG, EG, GG, IG, KG, MG, OG, QG, SG, UG, WG, YG, aG, cG, eG, gG, iG, kG, mG, oG, qG, sG, uG, OI, QI, SI, UI, WI, ZI, bI, dI, fI, hI, jI, lI, BJ, DJ, FJ, HJ, JJ, LJ, NJ, PJ, RJ, TJ, VJ, XJ | — | protein | 164 | — | E2IH77 |
| B1, D1, F1, H1, J1, L1, O1, Q1, S1, U1, W1, Y1, d1, f1, h1, j1, l1, n1, q1, s1, u1, w1, y1, 11, P2, R2, T2, V2, Y2, a2, c2, e2, g2, i2, k2, m2, B3, D3, F3, H3, J3, L3, N3, P3, R3, T3, V3, X3, B4, D4, F4, H4, J4, L4, O4, Q4, S4, U4, W4, Y4, d4, f4, h4, j4, l4, n4, q4, s4, u4, w4, y4, 14, I5, K5, P6, R6, T6, V6, Y6, a6, c6, e6, g6, i6, k6, m6, P7, R7, T7, V7, Y7, a7, c7, e7, g7, i7, k7, m7, D8, F8, H8, J8, L8, N8, P8, R8, T8, V8, X8, Z8, c8, e8, g8, i8, k8, m8, C9, E9, G9, I9, K9, M9, O9, Q9, S9, U9, W9, Y9, DA, FA, HA, JA, LA, NA, PA, RA, TA, VA, XA, ZA, cA, eA, gA, iA, kA, mA, PB, RB, TB, VB, YB, aB, cB, eB, gB, iB, kB, mB, KC, BD, DD, FD, HD, JD, LD, ND, PD, RD, TD, VD, XD, BE, DE, FE, HE, JE, LE, NE, PE, RE, TE, VE, XE, ZE, bE, dE, fE, hE, jE, lE, nE, pE, rE, tE, vE, PF, RF, TF, VF, YF, aF, cF, eF, gF, iF, kF, mF, BG, DG, FG, HG, JG, LG, NG, PG, RG, TG, VG, XG, ZG, bG, dG, fG, hG, jG, lG, nG, pG, rG, tG, vG, PI, RI, TI, VI, YI, aI, cI, eI, gI, iI, kI, mI, CJ, EJ, GJ, IJ, KJ, MJ, OJ, QJ, SJ, UJ, WJ, YJ | — | protein | 177 | — | P11393 |
| M1, 21, M4, 24 | — | protein | 238 | — | — |
| Z1, a1, Z4, a4, A5, B5, C5, F5, G5, H5, L5, AC, BC, CC, FC, GC, HC, LC | — | protein | 146 | — | P11393 |
| b1, b4 | — | protein | 323 | — | — |
| o1, o4 | — | protein | 212 | — | — |
| 31, 34 | — | protein | 285 | — | — |
| X2, X6, X7, XB, XF, XI | — | protein | 324 | — | — |
| A2, A6, A7, AB, AF, AI | — | protein | 257 | — | — |
| B2, BI | — | protein | 230 | — | W0RZ90 |
| C2, E2, G2, I2, K2, M2, C6, E6, G6, I6, K6, M6, C7, E7, G7, I7, K7, M7, CB, EB, GB, IB, KB, MB, CF, EF, GF, IF, KF, MF, CI, EI, GI, II, KI, MI | — | protein | 162 | — | W0RYI4 |
| D2, F2, H2, J2, L2, N2, D6, F6, H6, J6, L6, N6, D7, F7, H7, J7, L7, N7, DB, FB, HB, JB, LB, NB, DF, FF, HF, JF, LF, NF, DI, FI, HI, JI, LI, NI | — | protein | 172 | — | W0RZB2 |
| e3, eD | — | protein | 248 | — | — |
| Y3, YD | — | protein | 237 | — | — |
| B6, BB | — | protein | 231 | — | W0RZ90 |
| B7, BF | — | protein | 227 | — | W0RZ90 |
| b8, bA | — | protein | 380 | — | — |
| A8, AA, wE, xE, wG, xG | — | protein | 238 | — | — |
| B8, BA, yE, yG | — | protein | 250 | — | — |
| d9, dJ | — | protein | 285 | — | — |
| A9, AJ | — | protein | 256 | — | — |
| IC | — | protein | 176 | — | P11393 |
| zE, zG | — | protein | 370 | — | — |
| AH, CH, EH, GH, JH, KH, NH, PH, RH, TH, cH, eH, gH, iH, lH, mH, pH, rH, tH, vH | — | protein | 160 | — | W0RYM0 |
| DH, FH, BH, HH, IH, LH, MH, OH, QH, SH, UH, dH, fH, hH, jH, kH, nH, oH, qH, sH, uH, wH | — | protein | 161 | — | W0S279 |
| VH, xH | — | protein | 160 | — | W0S1U6 |
| WH, yH | — | protein | 173 | — | W0RZE2 |
| XH, zH | — | protein | 92 | — | — |
| YH, 1H | — | protein | 844 | — | W0RZJ2 |
| ZH, 2H | — | protein | 132 | — | — |
| aH, 3H | — | protein | 253 | — | — |
| bH, 4H | — | protein | 206 | — | — |
Ligands and binding sites
- PEB · Phycoerythrobilin · ligand · 1430 copies · chains A1, J1, B1, M1, C1, H1, D1, E1, F1, G1, L1, CD, I1, K1, KG, N1, W1, P1, Q1, O1, b1, U1, C9, R1, T1, S1, Z1, Y1, V1, X1, a1, c1, l1, e1, f1, d1, j1, o1, g1, i1, h1, n1, k1, m1, p1, y1, q1, 21, r1, w1, s1, t1, u1, v1, f2, 11, x1, z1, A2, l2, C2, D2, M2, E2, F2, K2, G2, H2, I2, J2, L2, N2, O2, Y2, X2, P2, Q2, V2, FF, PF, R2, S2, 34, T2, U2, a2, W2, Z2, eD, b2, k2, c2, d2, i2, e2, g2, h2, m2, j2, e3, WI, A3, J3, B3, Y3, C3, H3, G4, D3, E3, F3, G3, L3, P4, I3, K3, M3, V3, N3, O3, T3, lA, P3, Q3, R3, S3, X3, 31, U3, W3, HC, A4, J4, B4, M4, C4, H4, D4, E4, F4, L4, I4, K4, KE, N4, W4, Q4, O4, b4, U4, CJ, R4, T4, S4, Z4, Y4, V4, X4, 1H, a4, c4, l4, e4, f4, d4, j4, o4, g4, i4, h4, n4, k4, m4, p4, y4, q4, 24, r4, w4, s4, t4, u4, v4, fI, 14, dA, x4, z4, A5, B5, CB, DB, C5, F5, G5, H5, I5, 4H, NA, J5, ZH, K5, 3H, L5, A6, b6, k6, C6, D6, M6, G6, I6, J6, H6, E6, F6, K6, L6, N6, O6, Y6, Q6, R6, X6, P6, V6, BC, c6, S6, U6, T6, d9, a6, W6, E9, Z6, d6, i6, e6, f6, h6, g6, m6, j6, l6, A7, f7, h7, C7, D7, M7, E7, F7, K7, G7, H7, I7, J7, L7, N7, O7, Y7, Q7, R7, X7, P7, V7, S7, U7, T7, a7, g7, W7, Z7, b7, k7, d7, e7, c7, i7, m7, j7, l7, A8, d8, B8, C8, L8, E8, F8, D8, J8, b8, G8, I8, H8, N8, K8, M8, O8, X8, Q8, R8, P8, V8, S8, U8, T8, Z8, W8, Y8, a8, k8, e8, c8, i8, f8, h8, g8, m8, j8, l8, A9, T9, R9, B9, K9, D9, I9, F9, H9, G9, U9, M9, J9, L9, N9, W9, P9, Q9, O9, S9, Y9, V9, X9, AA, BA, CA, LA, AC, EA, FA, DA, JA, bA, GA, IA, HA, KA, MA, OA, XA, QA, RA, PA, VA, SA, UA, TA, ZA, WA, YA, aA, kA, eA, cA, iA, fA, hA, gA, mA, jA, AB, bB, MB, GB, IB, JB, KI, HB, EB, FB, KB, LB, NB, OB, YB, QB, RB, XB, PB, VB, cB, SB, UB, TB, dJ, aB, WB, ZB, kB, dB, iB, eB, fB, hB, gB, mB, jB, lB, CC, FC, GC, IC, bH, JC, 2H, KC, aH, LC, AD, JD, BD, YD, HD, DD, ED, FD, GD, LD, ID, KD, MD, VD, ND, OD, TD, PD, QD, RD, SD, XD, UD, WD, AE, JE, BE, zE, CE, HE, DE, EE, FE, yE, TE, GE, LE, EH, IE, ME, VE, OE, PE, NE, QE, SE, RE, XE, UE, WE, wE, YE, hE, aE, bE, ZE, fE, cE, KF, eE, dE, jE, gE, xE, iE, kE, tE, mE, nE, lE, rE, oE, qE, pE, vE, sE, uE, AF, cF, fF, hF, CF, DF, MF, EF, GF, HF, IF, JF, LF, NF, OF, YF, QF, RF, XF, VF, SF, TF, UF, aF, gF, WF, ZF, bF, kF, dF, eF, iF, mF, jF, lF, AG, JG, BG, zG, CG, HG, DG, EG, FG, yG, TG, GG, LG, gH, IG, MG, VG, OG, PG, NG, QG, SG, RG, XG, UG, wG, WG, YG, hG, aG, bG, ZG, fG, cG, eG, dG, jG, gG, xG, iG, kG, tG, mG, nG, lG, rG, oG, qG, pG, vG, sG, uG, AI, lI, jI, CI, DI, MI, EI, FI, GI, HI, II, JI, LI, NI, OI, YI, XI, PI, QI, VI, RI, SI, TI, UI, aI, ZI, bI, kI, cI, dI, iI, eI, gI, hI, mI, AJ, TJ, RJ, OJ, BJ, KJ, DJ, EJ, IJ, FJ, GJ, UJ, HJ, MJ, JJ, LJ, NJ, WJ, PJ, QJ, SJ, YJ, VJ, XJ
- CYC · Phycocyanobilin · ligand · 120 copies · chains C2, F2, X2, D2, E2, H2, B2, G2, I2, L2, J2, K2, N2, M2, B6, J6, N6, C6, F6, X6, D6, E6, H6, G6, I6, L6, K6, M6, C7, F7, X7, D7, E7, H7, G7, B7, I7, L7, J7, M7, K7, N7, BB, JB, CB, FB, XB, DB, EB, HB, GB, IB, LB, KB, NB, MB, CF, FF, XF, DF, GF, EF, HF, BF, IF, LF, JF, MF, KF, NF, AH, FH, CH, BH, YH, DH, EH, GH, IH, HH, JH, KH, MH, LH, XH, bH, zG, NH, OH, PH, SH, QH, RH, UH, TH, 3H, VH, WH, cH, fH, dH, 1H, eH, hH, gH, iH, kH, jH, lH, bA, mH, oH, nH, zH, 4H, zE, pH, qH, xH, rH, uH, sH, tH, wH, aH, vH, BI, 2H, yH, CI, FI, XI, DI, EI, HI, GI, II, LI, JI, KI, NI, MI
- PUB · Phycourobilin · ligand · 48 copies · chains A1, C1, M1, I1, K1, x1, z1, 21, p1, r1, A2, f2, h2, b2, d2, I3, K3, Y3, A3, C3, A4, C4, M4, I4, K4, x4, z4, 24, p4, r4, A6, f6, h6, j6, l6, A7, j7, l7, b7, d7, A8, l8, f8, h8, B8, S8, U8, O8, Q8, A9, V9, X9, N9, P9, AA, lA, fA, hA, BA, SA, UA, OA, QA, AB, fB, hB, jB, lB, ID, KD, YD, AD, CD, gE, iE, wE, YE, aE, xE, kE, mE, sE, uE, ME, OE, yE, UE, WE, AF, jF, lF, bF, dF, gG, iG, wG, YG, aG, xG, kG, mG, sG, uG, MG, OG, yG, UG, WG, AI, fI, hI, bI, dI, AJ, VJ, XJ, NJ, PJ
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- P11393 · AlphaFold monomer V2.0 prediction for B-phycoerythrin beta chain (P11393) · a predicted model of the same protein · chain Z1 against A, TM-score 0.96
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt E2IH77
- Every structure of UniProt P11393
- Every structure of UniProt W0RZ90
- Every structure of UniProt W0RYI4
- Every structure of UniProt W0RZB2
- Every structure of UniProt W0RYM0
- Every structure of UniProt W0S279
- Every structure of UniProt W0S1U6
- Every structure of UniProt W0RZE2
- Every structure of UniProt W0RZJ2
- Elsewhere: RCSB PDB 6KGX · PDBe 6KGX · UniProt E2IH77 · UniProt P11393 · UniProt W0RZ90 · UniProt W0RYI4 · UniProt W0RZB2 · UniProt W0RYM0 · UniProt W0S279 · UniProt W0S1U6 · UniProt W0RZE2 · UniProt W0RZJ2
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